JP2010514777A - Methods for monitoring biomarkers using histone deacetylase inhibitors in combination therapy - Google Patents

Abstract

In a method of using at least one histone deacetylase inhibitor, a method of monitoring a decrease in cellular DNA repair activity using at least one biomarker to reduce cellular DNA repair activity, in combination therapy A method of treating cancer by using at least one histone deacetylase inhibitor to reduce cellular DNA repair activity, at least one histone deacetylase inhibitor is a DNA repair involving RAD51 Methods of combination therapy that interfere with the mechanism, methods of predicting the induction time between a first administration of at least one histone deacetylase inhibitor and a second treatment of at least one other therapeutic measure, and combinations A pharmaceutical composition for therapy is provided.
[Selection figure] None

Description

Described herein is a method of using at least one histone deacetylase inhibitor to reduce cellular DNA repair activity. Also described is a method of monitoring a decrease in cellular DNA repair activity using at least one biomarker.
(Cross-reference of related applications)
The present application is US Provisional Application No. 60 / 871,900, filed on Dec. 26, 2006, entitled “Method of Monitoring Biomarkers Using Histone Deacetylase Inhibitor in Combination Therapy” (the application) Are incorporated herein by reference).

  DNA damage results in chromosomal instability, tumorigenesis, cell death, and severe cellular dysfunction. DNA repair systems are critical to living cell survival. The two main DNA repair mechanisms involved in repairing double-stranded DNA breaks are homologous recombination (HR) and non-homologous end joining (NHEJ). The eukaryotic RAD51 gene is an ortholog of Escherichia coli RecA, and the gene product RAD51 protein plays a central role in homologous recombination.

  Many therapeutic measures, such as anticancer drugs, exert a therapeutic effect by their ability to produce DNA damage to cells. If cells such as cancer cells have an active DNA repair mechanism, the therapeutic effect of such treatment may be diminished and higher doses may be required to achieve the desired therapeutic effect.

  Described herein is a method of using at least one histone deacetylase inhibitor to reduce cellular DNA repair activity. Also described herein is a method for monitoring a decrease in cellular DNA repair activity using at least one biomarker.

  Described herein is a method of treating cancer by using at least one histone deacetylase inhibitor to reduce cellular DNA repair activity in combination therapy. A method in combination therapy in which at least one histone deacetylase inhibitor interferes with the DNA repair mechanism involving RAD51 is described. A method for predicting the time between a first administration of at least one histone deacetylase inhibitor and a second treatment of at least one other therapeutic measure is also described. Also described are pharmaceutical compositions for combination therapy.

One aspect is a method of treating a disease, disorder or condition associated with a defect in non-homologous end joining of DNA comprising:
(A) prevent the formation of RAD51 lesions that inhibit the activity of at least one therapeutically effective amount of RAD51 in a human patient suffering from a disease, disorder or condition associated with a defect in non-homologous end joining of DNA ( disrupt), or administering an agent that prevents the construction of a functional repair complex for homologous recombination of DNA;
(B) administering to the human patient a treatment capable of damaging cellular DNA;
It is a method including.

  In another embodiment, the agent prevents the construction of a functional repair complex for homologous recombination of DNA. In another embodiment, an agent that inhibits RAD51 activity reduces cellular levels of RAD51. In another embodiment, the agent that prevents the construction of a functional repair complex for homologous recombination of DNA is at least one therapeutically effective amount of a histone deacetylase inhibitor, or a pharmaceutically acceptable agent thereof. It is an acceptable derivative.

  In another embodiment, the agent that prevents the formation of RAD51 lesions is a therapeutically effective amount of at least one histone deacetylase inhibitor, or a pharmaceutically acceptable derivative thereof. In another embodiment, the defect in non-homologous end joining of DNA comprises a defect in a gene selected from the group consisting of Ku70, Ku80, Ku86, Ku, PRKDC, LIG4, XRCC4, DCLRE1C and XLF. In another embodiment, the disease, disorder or condition is cancer. In another embodiment, the disease, disorder or condition is selected from Burkitt lymphoma, chronic myelogenous leukemia and B cell lymphoma. In another embodiment, the DNA damaging agent is administered when RAD51 expression is within a predetermined range. In another embodiment, the therapeutically effective amount of at least one histone deacetylase inhibitor is about 0.2 mg to about 2000 mg.

  In another embodiment, the predetermined range of RAD51 expression levels is less than 70% compared to the expression level of RAD51 prior to administration of the at least one histone deacetylase inhibitor. In another embodiment, the cancer is breast cancer, colon cancer, colorectal cancer, non-small cell lung cancer, small cell lung cancer, liver cancer, ovarian cancer, prostate cancer, cervical cancer, bladder cancer, gastric cancer, gastrointestinal stromal tumor Pancreatic cancer, germ cell tumor, mast cell tumor, neuroblastoma, mastocytosis, testicular cancer, glioblastoma, astrocytoma, lymphoma, melanoma, myeloma, acute myeloid leukemia (AML), Selected from the group consisting of acute lymphoblastic leukemia (ALL), myelodysplastic syndrome and chronic myeloid leukemia.

  In another embodiment, the treatment capable of damaging cellular DNA includes radiation therapy, administration of a pharmaceutically effective amount of at least one anti-cancer agent, a combined cancer treatment scheme, or any combination thereof. In another embodiment, the treatment capable of damaging cellular DNA is selected from the group consisting of radiotherapy or topoisomerase inhibitors, tubulin interactors, DNA interacting agents, DNA alkylating agents and platinum complexes. Administration of at least one pharmaceutically effective amount of the drug.

  In another embodiment, the treatment capable of damaging cellular DNA includes radiation therapy. In another embodiment, the anti-cancer agent is a cytotoxic / cytostatic agent, anti-proliferative agent, prenyl protein transferase inhibitor, HMG-CoA reductase inhibitor, nitrogen mustard, nitrosourea, angiogenesis inhibitor, cell Inhibitors of proliferation and survival signaling pathways, apoptosis inducers, agents that interfere with cell cycle checkpoints, biphosphonates, or any combination thereof.

Another aspect is a method of treating cancer comprising:
(A) administering to a human patient suffering from cancer a therapeutically effective amount of at least one histone deacetylase inhibitor, or a pharmaceutically acceptable derivative thereof;
(B) administering at least one other anti-cancer treatment when the expression level of the predetermined biomarker is within a predetermined range;
It is a method including.

  In another embodiment, the cancer is breast cancer, colon cancer, colorectal cancer, non-small cell lung cancer, small cell lung cancer, liver cancer, ovarian cancer, prostate cancer, cervical cancer, bladder cancer, gastric cancer, gastrointestinal stromal tumor Pancreatic cancer, germ cell tumor, mast cell tumor, neuroblastoma, mastocytosis, testicular cancer, glioblastoma, astrocytoma, lymphoma, melanoma, myeloma, acute myeloid leukemia (AML), Selected from the group consisting of acute lymphoblastic leukemia (ALL), myelodysplastic syndrome and chronic myeloid leukemia.

  In another embodiment, the cancer is associated with a loss of non-homologous end joining of DNA. In another embodiment, the defect in non-homologous end joining of DNA comprises a defect in a gene selected from the group consisting of Ku70, Ku80, Ku86, Ku, PRKDC, LIG4, XRCC4, DCLRE1C and XLF. In another embodiment, the disease, disorder or condition is selected from Burkitt lymphoma, chronic myelogenous leukemia and B cell lymphoma. In another embodiment, the cancer is associated with overexpression of RAD51. In another embodiment, the cancer is associated with overexpression of homologous recombination of DNA or involves homologous recombination of DNA as a pathogenesis of cancer. In another embodiment, the therapeutically effective amount of at least one histone deacetylase inhibitor is about 0.2 mg to about 2000 mg.

  In another embodiment, the therapeutically effective amount is sufficient to prevent the construction of a functional repair complex for homologous recombination of DNA. In another embodiment, the therapeutically effective amount is sufficient to reduce the cellular level of RAD51 in the cell. In another embodiment, the therapeutically effective amount is sufficient to prevent the formation of RAD51 lesions in the cells.

  In another embodiment, the predetermined biomarker is RAD51. In another embodiment, the predetermined biomarker is RAD51 lesion disruption. In another embodiment, the predetermined range of biomarker expression levels is less than 70% compared to the expression level of the biomarker prior to administration of the at least one histone deacetylase inhibitor. In another embodiment, the at least one other anti-cancer treatment is radiation therapy, administration of a pharmaceutically effective amount of at least one anti-cancer agent, a known combination scheme for cancer treatment, or any of these Includes combinations.

  In another embodiment, the at least one other anti-cancer treatment includes a treatment capable of damaging cellular DNA. In another embodiment, the treatment capable of damaging cellular DNA is radiation therapy, or pharmaceutically effective amounts of topoisomerase inhibitors, tubulin interactors, DNA interacting agents, DNA alkylating agents and platinum complexes. Administration of at least one drug selected from the group consisting of:

  In another embodiment, the at least one other anti-cancer treatment includes radiation therapy. In another embodiment, the anti-cancer agent is a cytotoxic / cytostatic agent, anti-proliferative agent, prenyl protein transferase inhibitor, HMG-CoA reductase inhibitor, nitrogen mustard, nitrosourea, angiogenesis inhibitor, cell Inhibitors of proliferation and survival signaling pathways, apoptosis inducers, agents that interfere with cell cycle checkpoints, biphosphonates, or any combination thereof.

Another aspect is a method of using a histone deacetylase inhibitor comprising:
(A) administering to the subject a therapeutically effective amount of at least one histone deacetylase inhibitor, or a pharmaceutically acceptable derivative thereof;
(B) monitoring a decrease in the expression level of a given biomarker in at least one cell of the subject;
(C) administering at least one other therapeutic measure when the expression level of the biomarker is within a predetermined range;
It is a method including.

  In another embodiment, the subject is a human patient. In another embodiment, the subject suffers from a disease, disorder or condition associated with a defect in non-homologous end joining of DNA. In another embodiment, the defect in non-homologous end joining of DNA comprises a defect in a gene selected from the group consisting of Ku70, Ku80, Ku86, Ku, PRKDC, LIG4, XRCC4, DCLRE1C and XLF.

  In another embodiment, the disease, disorder or condition is selected from Burkitt lymphoma, chronic myelogenous leukemia and B cell lymphoma. In another embodiment, the subject suffers from a disease, disorder or condition associated with RAD51 overexpression. In another embodiment, the subject suffers from a disease, disorder or condition associated with overexpression of homologous recombination of DNA or involving homologous recombination of DNA as the etiology of the disease, disorder or condition. In another embodiment, the disease, disorder or condition is selected from Bloom syndrome or viral infection. In another embodiment, the therapeutically effective amount of at least one histone deacetylase inhibitor is about 0.2 mg to about 2000 mg.

  In another embodiment, the predetermined biomarker is RAD51. In another embodiment, the predetermined range of biomarker expression levels is less than about 70% compared to the expression level of the biomarker prior to administration of the at least one histone deacetylase inhibitor. In another embodiment, the at least one other therapeutic measure is radiation therapy, surgery, gene therapy, siRNA or RNAi therapy, administration of at least one pharmaceutically effective amount of an anticancer agent, for cancer treatment. It is selected from the group consisting of known combination schemes and any combination thereof.

  In another embodiment, the at least one other therapeutic measure includes a treatment capable of damaging cellular DNA. In another embodiment, the treatment capable of damaging cellular DNA is selected from the group consisting of radiotherapy or topoisomerase inhibitors, tubulin interactors, DNA interacting agents, DNA alkylating agents and platinum complexes. Administration of at least one pharmaceutically effective amount of the drug.

  In another embodiment, the at least one other therapeutic measure includes radiation therapy. In another embodiment, the anti-cancer agent is a cytotoxic / cytostatic agent, anti-proliferative agent, prenyl protein transferase inhibitor, HMG-CoA reductase inhibitor, nitrogen mustard, nitrosourea, angiogenesis inhibitor, cell Inhibitors of proliferation and survival signaling pathways, apoptosis inducers, agents that interfere with cell cycle checkpoints, biphosphonates, or any combination thereof.

Another aspect is a method of treating a disease, disorder or condition associated with overexpression of RAD51 comprising:
(A) In a human patient suffering from a disease, disorder or condition associated with overexpression of RAD51, inhibit the activity of at least one therapeutically effective amount of RAD51, prevent the formation of RAD51 lesions, or DNA homology Administering an agent that prevents the construction of a functional repair complex for genetic recombination;
(B) administering to the human patient a treatment capable of damaging cellular DNA;
It is a method including.

  In another embodiment, the agent prevents the construction of a functional repair complex for homologous recombination of DNA. In another embodiment, an agent that inhibits RAD51 activity reduces cellular levels of RAD51. In another embodiment, the agent prevents the formation of RAD51 lesions.

  In another embodiment, the agent that prevents the construction of a functional repair complex for homologous recombination of DNA is a therapeutically effective amount of at least one histone deacetylase inhibitor, or a pharmaceutically acceptable agent thereof. It is an acceptable derivative. In another embodiment, the disease, disorder or condition is cancer. In another embodiment, the DNA damaging agent is administered when RAD51 expression is within a predetermined range. In another embodiment, the therapeutically effective amount of at least one histone deacetylase inhibitor is about 0.2 mg to about 2000 mg.

  In another embodiment, the predetermined range of RAD51 expression levels is less than about 70% compared to the expression level of RAD51 prior to administration of the at least one histone deacetylase inhibitor. In another embodiment, the cancer is breast cancer, colon cancer, colorectal cancer, non-small cell lung cancer, small cell lung cancer, liver cancer, ovarian cancer, prostate cancer, cervical cancer, bladder cancer, gastric cancer, gastrointestinal stromal tumor Pancreatic cancer, germ cell tumor, mast cell tumor, neuroblastoma, mastocytosis, testicular cancer, glioblastoma, astrocytoma, lymphoma, melanoma, myeloma, acute myeloid leukemia (AML), Selected from the group consisting of acute lymphoblastic leukemia (ALL), myelodysplastic syndrome and chronic myeloid leukemia.

  In another embodiment, the treatment capable of damaging cellular DNA comprises radiation therapy or administration of a pharmaceutically effective amount of at least one anticancer agent, known combination schemes for cancer treatment, or any of these Includes combinations. In another embodiment, the treatment capable of damaging cellular DNA is selected from the group consisting of radiotherapy or topoisomerase inhibitors, tubulin interactors, DNA interacting agents, DNA alkylating agents and platinum complexes. Administration of at least one pharmaceutically effective amount of the drug.

  In another embodiment, the treatment capable of damaging cellular DNA includes radiation therapy. In another embodiment, the anti-cancer agent is a cytotoxic / cytostatic agent, anti-proliferative agent, prenyl protein transferase inhibitor, HMG-CoA reductase inhibitor, nitrogen mustard, nitrosourea, angiogenesis inhibitor, cell Inhibitors of proliferation and survival signaling pathways, apoptosis inducers, agents that interfere with cell cycle checkpoints, biphosphonates, or any combination thereof.

Another aspect is a method of treating a disease, disorder or condition associated with overexpression of homologous recombination of DNA or involving the homologous recombination of DNA as the etiology.
(A) In a human patient, inhibit the activity of at least one therapeutically effective amount of RAD51, prevent the formation of RAD51 foci, or construct a functional repair complex for homologous recombination of DNA. Administering an interfering agent, wherein the human patient is suffering from a disease, disorder or condition associated with overexpression of homologous recombination of DNA or the disease, disorder or condition is homologous recombination Having an etiology involving, and
(B) administering to the human patient a treatment capable of damaging cellular DNA;
It is a method including.

  In another embodiment, the agent prevents the construction of a functional repair complex for homologous recombination of DNA. In another embodiment, an agent that inhibits RAD51 activity reduces cellular levels of RAD51. In another embodiment, the agent prevents the formation of RAD51 lesions.

  In another embodiment, the agent that prevents the construction of a functional repair complex for homologous recombination of DNA is a therapeutically effective amount of at least one histone deacetylase inhibitor, or a pharmaceutically acceptable agent thereof. It is an acceptable derivative. In another embodiment, the disease, disorder or condition is cancer. In another embodiment, the disease, disorder or condition is a viral infection. In another embodiment, the disease, disorder, or condition is Bloom syndrome. In another embodiment, the DNA damaging agent is administered when RAD51 expression is within a predetermined range. In another embodiment, the therapeutically effective amount of at least one histone deacetylase inhibitor is about 0.2 mg to about 2000 mg.

  In another embodiment, the predetermined range of RAD51 expression levels is less than about 70% compared to the expression level of RAD51 prior to administration of the at least one histone deacetylase inhibitor. In another embodiment, the cancer is breast cancer, colon cancer, colorectal cancer, non-small cell lung cancer, small cell lung cancer, liver cancer, ovarian cancer, prostate cancer, cervical cancer, bladder cancer, gastric cancer, gastrointestinal stromal tumor Pancreatic cancer, germ cell tumor, mast cell tumor, neuroblastoma, mastocytosis, testicular cancer, glioblastoma, astrocytoma, lymphoma, melanoma, myeloma, acute myeloid leukemia (AML), Selected from the group consisting of acute lymphoblastic leukemia (ALL), myelodysplastic syndrome and chronic myeloid leukemia.

  In another embodiment, the treatment capable of damaging cellular DNA comprises radiation therapy or administration of at least one pharmaceutically effective amount of an anticancer agent, known combination schemes for cancer treatment, or any of these Includes combinations. In another embodiment, the treatment capable of damaging cellular DNA is selected from the group consisting of radiotherapy or topoisomerase inhibitors, tubulin interactors, DNA interacting agents, DNA alkylating agents and platinum complexes. Administration of at least one pharmaceutically effective amount of the drug.

  In another embodiment, the treatment capable of damaging cellular DNA includes radiation therapy. In another embodiment, the anti-cancer agent is a cytotoxic / cytostatic agent, anti-proliferative agent, prenyl protein transferase inhibitor, HMG-CoA reductase inhibitor, nitrogen mustard, nitrosourea, angiogenesis inhibitor, cell Inhibitors of proliferation and survival signaling pathways, apoptosis inducers, agents that interfere with cell cycle checkpoints, biphosphonates, or any combination thereof.

Another embodiment is a method of treating cancer comprising:
(A) In a human patient, inhibit the activity of at least one therapeutically effective amount of RAD51, prevent the formation of RAD51 foci, or construct a functional repair complex for homologous recombination of DNA. The human patient suffers from a cancer that does not involve telomerase but rather uses a mechanism known as the alternative telomere elongation (ATL) pathway to maintain its telomere length. Being administered, and
(B) administering an additional anticancer agent to the human patient;
It is a method including.

  12% of all cancers and more than 50% of sarcomas, thyroid cancers, osteosarcomas and glioblastomas are included in the cancer classification described above. In particular, homologous recombination including RAD51 is involved in the ALT pathway. RAD51 is found in ALT-related PML bodies (APB), and the mechanism of ALT depends on DNA double strand breakage mechanisms, especially homologous recombination and especially RAD51. HDAC inhibitors that misregulate RAD51 would be particularly useful in ALT positive cancers. In some embodiments, ALT is screened by a relatively simple and robust assay.

One aspect is a method of treating a disease, disorder or condition associated with a defect in non-homologous end joining of DNA comprising:
a) preventing the interaction of BRCA1 and RAD51 in a patient suffering from a disease, disorder or condition associated with a defect in non-homologous end joining of DNA, inhibiting the activity of at least one therapeutically effective amount of BRCA1; Or administering an agent that prevents the construction of a functional repair complex for homologous recombination involving BRCA1;
b) administering to the patient a treatment capable of damaging cellular DNA;
It is a method including.

Another aspect is:
(A) an agent that inhibits the activity of at least one therapeutically effective amount of RAD51, prevents the formation of RAD51 foci, or prevents the construction of a functional repair complex for homologous recombination of DNA. A first coating for one release;
(B) a second coating for a second release of at least one other therapeutic agent;
A pharmaceutical composition comprising

Another aspect is:
(A) building a functional repair complex for homologous recombination for inhibiting the activity of at least one therapeutically effective amount of BRCA1, preventing the interaction of BRCA1 and RAD51, or involving BRCA1 With a first coating for a first release of the blocking agent,

(B) a second coating for a second release of at least one other therapeutic agent;
A pharmaceutical composition comprising

  In another embodiment, the second release occurs after the first release. In another embodiment, the agent that inhibits the activity of RAD51 is at least one histone deacetylase inhibitor, or a pharmaceutically acceptable derivative thereof. In another embodiment, the therapeutically effective amount of at least one histone deacetylase inhibitor is about 0.2 mg to about 2000 mg.

  In a further embodiment, the second release occurs after the first release. In yet a further embodiment, the agent that inhibits the activity of BRCA1 is at least one histone deacetylase inhibitor, or a pharmaceutically acceptable derivative thereof. In another embodiment, the therapeutically effective amount of at least one histone deacetylase inhibitor is about 0.2 mg to about 2000 mg.

  In another embodiment, the at least one other therapeutic agent comprises an agent capable of damaging cellular DNA. In another embodiment, the agent capable of damaging cellular DNA is selected from the group consisting of topoisomerase inhibitors, tubulin interactors, DNA interacting agents, DNA alkylating agents and platinum complexes.

  In another embodiment, the at least one other therapeutic agent is a cytotoxic / cytostatic agent, an antiproliferative agent, a prenyl protein transferase inhibitor, an HMG-CoA reductase inhibitor, a nitrogen mustard, a nitrosourea. An angiogenesis inhibitor, an inhibitor of cell proliferation and survival signaling pathway, an apoptosis-inducing agent, an agent that interferes with the cell cycle checkpoint, a biphosphonate, or any combination thereof.

  In any of the foregoing embodiments and aspects, the at least one histone deacetylase inhibitor is from carboxylates, short chain fatty acids, hydroxamic acids, electrophilic ketones, epoxides, cyclic peptides and benzamides. Selected from the group consisting of

  In further embodiments, the histone deacetylase inhibitor is US Patent Application Nos. 10 / 818,755, 10 / 537,115, 10 / 922,119, 11 / 100,781, or PCT. A compound selected from the compounds or formulas disclosed in patent application No. PCT / US2005 / 046255.

In a further embodiment, the histone deacetylase inhibitor has the formula (A):
(Where
Q is optionally substituted C _5-12 aryl, or optionally substituted C _5-12 heteroaryl,
L is a linker having at least 4 atoms;
R ¹ is H or alkyl)
And a pharmaceutically acceptable salt thereof, a pharmaceutically acceptable N-oxide, a pharmaceutically active metabolite, a pharmaceutically acceptable prodrug, and a pharmaceutically acceptable solvent. It is a Japanese product.

In another embodiment, the histone deacetylase inhibitor has the formula (I):
(Where
R ¹ is hydrogen or alkyl;
X is —O—, —NR ² —, or —S (O) _n, where n is 0-2 and R ² is hydrogen or alkyl;
Y is alkylene optionally substituted with cycloalkyl, optionally substituted phenyl, alkylthio, alkylsulfinyl, alkylsulfonyl, optionally substituted phenylalkylthio, optionally substituted phenylalkylsulfonyl, hydroxy, or optionally Substituted phenoxy,
Ar ¹ is phenylene or heteroarylene, wherein said Ar ¹ is optionally substituted with one or two groups independently selected from alkyl, halo, hydroxy, alkoxy, haloalkoxy or haloalkyl And
R ³ is hydrogen, alkyl, hydroxyalkyl, or optionally substituted phenyl, and Ar ² is aryl, aralkyl, aralkenyl, heteroaryl, heteroaralkyl, heteroaralkenyl, cycloalkyl, cycloalkylalkyl, Heterocycloalkyl or heterocycloalkylalkyl. )
And a single stereoisomer, a single geometric isomer, or a mixture thereof, or a pharmaceutically acceptable salt thereof.

In another embodiment, the histone deacetylase inhibitor is of the formula (a)
Or a pharmaceutically acceptable salt thereof.

In another embodiment, the histone deacetylase inhibitor is of the formula (b)
Or a pharmaceutically acceptable salt thereof.

In another embodiment, the histone deacetylase inhibitor is of formula (c)
Or a pharmaceutically acceptable salt thereof.

In another embodiment, the histone deacetylase inhibitor is of the formula (d)
Or a pharmaceutically acceptable salt thereof.

In another embodiment, the histone deacetylase inhibitor is of the formula (e)
Or a pharmaceutically acceptable salt thereof.

  One aspect is a method of selecting a cancer treatment for a patient in need of cancer treatment, a) determining the expression level of RAD51 mRNA, or RAD51 protein level in at least one cancer cell from the patient; B) If the expression level of RAD51 mRNA or the level of RAD51 protein in the biological sample exceeds the expression level of RAD51 mRNA or the level of RAD51 protein in the standard data, at least one histone deacetylase inhibitor is effective for treatment. Suggesting that it is.

  Other features and objects will be apparent from the description and from the claims. One or more detailed embodiments are described in conjunction with the accompanying drawings and the following description. Other features and objects of the methods and pharmaceutical compositions described herein will be apparent from the description and drawings, and from the claims.

Figure 3 shows the effect of ionizing radiation after pretreatment of a HDAC inhibitor test compound having the structure of formula (A) or formula (I). 3-((Dimethylamino) methyl) -N- (2- (4- (4- ()) at both mRNA (left) and protein (right) levels for up to 24 hours in the HCT-116 colon tumor cell line in vitro. 2 shows the time course of RAD51 down-regulation by hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide. Also shown are RAD51 and actin levels after extraction of tumors from HCT-116 mouse xenografts with different dosage regimens. 1X animals received a single oral dose 4 hours before the end of the experiment, 2X animals received a single oral dose 28 hours before the end of the experiment, and a second dose 6 hours later. It was administered in the same way as 2X and received the third dose the next morning, ie 24 hours after the first dose, 4 hours before the end of the study. Fold changes in protein level were quantified using Odyssey software and normalized to the level of actin loading control. Figure 9 shows baseline RAD51 expression levels normalized to actin in non-Hodgkin's lymphoma cells for a minimal level in HH, a cutaneous T-cell lymphoma cell line, by Western blot. RAD51 expression by immunohistochemical staining in human DLBCL tumor samples from tissue microarray (TMA) containing 229 primary tumor parts (138 follicular lymphomas and 91 DLBCL). 78% of samples of each tumor type in TMA expressed RAD51 at moderate to high levels. Down-regulation of NHL cell lines treated with 3-((dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide in a dose-dependent manner for 24 hours RAD51 protein level is shown, HH shows minimal effect. Cell lines treated with 3-((dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide, and then RAD51 mRNA analyzed by Taqman RT-PCR Show. According to Western blot analysis, 3-((dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide doubled RAD51 mRNA expression in most cell lines. The HH strain did not show a decrease in RAD51. A dose-dependent increase in apoptotic cell death was shown to be observed in all cell lines except the HH lymphoma cell line, with lower levels of apoptosis observed at 24 hours in all cell lines. The baseline RAD51 expression level by Western blot is shown. The reduced level of RAD51 protein in the treated cells is shown. FIG. 5 shows that RAD51 protein and mRNA levels are reduced in correlation with% apoptosis. A correlation plot of mRNA expression levels for% apoptosis is shown, and the most sensitive and resistant cell lines are shown in the frame. 3-((dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide and doxorubicin administered simultaneously in non-Hodgkin cell lines DHL-4, DLCL2 and HH The effect of the combination is shown.

  Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.

  It should be understood that the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the invention as claimed. In this application, the use of the singular includes the plural unless specifically stated otherwise. It should be noted that the singular forms “a”, “an”, and “the”, as used in the specification and the appended claims, include the plural unless the context clearly dictates otherwise. In this application, unless stated otherwise, when “or” is used, this means “and / or”. Further, the terms “including” and other forms, such as “include”, “included”, are not limiting.

  The disruption of homologous recombination (HR) by HDAC inhibitors allows treatment with low doses of DNA-interacting agents or anticancer agents after pretreatment with HDAC inhibitors. In other embodiments, HR is directly disrupted by an HDAC inhibitor, and thus HR-mediated DNA repair is inhibited by an HDAC inhibitor. In a further embodiment, HR disruption is observed by monitoring RAD51 foci formation in the cell nucleus. In still further embodiments, DNA double strand breaks (DSB) are induced by ionizing radiation, and the radiation-induced DSB is normally repaired by HR during S phase. Since RAD51 lesions are disrupted by cells pretreated with HDAC inhibitors, DSB repair by HR is inhibited, and the cells become more sensitive to DNA interacting agents such as certain anticancer agents.

  Furthermore, RAD51 protein and mRNA levels are reduced after treatment with HDAC inhibitors. Since DNA DSB induced by radiation can be repaired by HR after HDAC inhibitor treatment, DNA damage induced by DNA-interactive cancer therapeutics cannot be repaired by HR. Thus, tumor cells pre-treated with at least one HDAC inhibitor can be used for subsequent treatment of a therapy that causes DSB to be repaired by (1) radiation, (2) DNA interacting agents and / or (3) HR. It will be oversensitive. In another embodiment, a synergistic effect is observed between at least one HDAC inhibitor and radiation, or between at least one HDAC inhibitor and one or more platinum agents.

  Pre-treating a cancer patient with an appropriate dose of at least one HDAC inhibitor and planning subsequent treatment until HR is disrupted by the effects of the at least one HDAC inhibitor Is provided. In another embodiment, HR perturbation in a cancer patient is determined by: (1) a direct measurement of RAD51 foci formation in the blood, (2) measurement of any surrogate biomarker in the blood that reflects RAD51 foci formation in the tumor ( For example, RAD51 levels in PBMC), (3) monitored by measurement of any marker that reflects the establishment of a mechanism for homologous repair.

  In other embodiments, patients with tumors that overexpress RAD51 are specifically targeted by the methods provided herein. Tumors that overexpress RAD51 usually have increased HR activity and are resistant to DNA interacting or damaging agents. For example, most pancreatic tumors are tumors that overexpress RAD51. In some embodiments herein, pretreatment with at least one HDAC inhibitor at least partially overcome resistance to DNA interacting or damaging agents used for subsequent therapeutic measures. A method is provided.

  In some embodiments, patients suffering from tumors that are deficient in non-homologous end joining (NHEJ) are specifically targeted by the methods provided herein. Since the HR mechanism of DNA repair is the dominant pathway of DNA repair in tumors with certain defects in NHEJ, in some embodiments, disruption of HR in these tumor cells completely blocks DNA repair activity. These tumor cells are rendered sensitive to DNA interacting agents or DNA damaging agents used in subsequent therapeutic measures. For example, tumor cells with mutations in Ku play an important role in NHEJ and are very sensitive to HDAC inhibitor treatment.

In other embodiments, patients with any disease involving HR as an etiology are also specifically targeted by the methods provided herein. For example, the HIV virus is used as the host HR during genome integration. Thus, in some embodiments, pretreatment with an HDAC inhibitor is also useful for viral diseases.
Definition:

  Unless otherwise stated, the following terms used in the specification and claims are defined for the purposes of this application and have the following meanings.

  In one embodiment, “alkyl” is a straight-chain saturated monovalent hydrocarbon radical of 1 to 6 carbon atoms or a branched and saturated monovalent hydrocarbon radical of 3 to 6 carbon atoms. For example, methylethyl, propyl, 2-propyl, butyl (including all isomers), pentyl (including all isomers), and the like.

In another embodiment, “aryl” refers to a monovalent monocyclic or bicyclic aromatic hydrocarbon radical of 6 to 12 ring atoms, such as phenyl, naphthyl or anthracenyl. Unless stated otherwise, the aryl ring is optionally alkyl, alkoxy, halo, haloalkyl, haloalkoxy, amino, alkylamino, dialkylamino, hydroxy, hydroxyalkyl, hydroxyalkyloxy, hydroxyalkoxyalkyl, alkoxyalkyloxyalkyl. Optionally substituted phenyl, optionally substituted phenylalkyl, optionally substituted heteroaryl, cycloalkyloxy, cycloalkenyloxy, optionally substituted phenylcarbonylamino, optionally substituted heteroaryloxy, Optionally substituted heteroaralkyloxy, aminoalkyl, aminoalkoxy, alkoxyalkyl, alkoxyalkyloxy, methylenedioxy, haloalkoxyalkyl, optionally substituted phenyl Oxyalkyl, optionally substituted heteroaryloxyalkyl, optionally substituted heterocycloalkyl, optionally substituted heterocycloalkyloxyalkyl, optionally substituted heterocycloalkylalkyl, optionally substituted heterocyclo Alkylalkyloxy, optionally substituted heterocycloalkyloxy, -alkylene-S (O) _n -R ^a , wherein n is 0 to 2, and R ^a is alkyl, haloalkyl, hydroxyalkyl, alkoxy Alkyl, optionally substituted phenyl, optionally substituted phenylalkyl, optionally substituted heteroaryl, or optionally substituted heteroaralkyl), -alkylene-NHSO ₂ -R ^b , where R ^b is substituted alkyl, haloalkyl, optionally phenyl Optionally substituted phenylalkyl, optionally substituted heteroaryl, optionally substituted heteroaralkyl, or optionally substituted heterocycloalkyl), - alkylene -NHCO-R c ^(wherein, R ^c Is alkyl, haloalkyl, optionally substituted phenyl, optionally substituted phenylalkyl, optionally substituted heteroaryl, optionally substituted heteroaralkyl, or optionally substituted heterocycloalkyl), or - _(alkylene) in n1 -CONR ^d R ^e (wherein, n1 is 0 or 1, ^{R d} and ^{R e} are independently hydrogen, alkyl, haloalkyl, hydroxyalkyl, alkoxyalkyl, aminoalkyl, optionally Substituted phenyl, optionally substituted phenylalkyl, optionally substituted Heteroaryl, optionally substituted heteroaralkyl, or optionally substituted heterocycloalkylalkyl, or R ^d and R ^e together with the nitrogen atom to which they are attached form a heterocycloalkyl (Wherein the alkyl chain in haloalkoxyalkyl, optionally substituted phenyloxyalkyl, optionally substituted heteroaryloxyalkyl, or aminoalkyl is optionally substituted with 1 or 2 fluoro) Substituted with one, two or three substituents independently selected from. In some embodiments, the substituents are independently methoxy, methyl, ethyl, chloro, trifluoromethyl, fluoro, 2-methoxyethoxy, 2- (morpholin-4-yl) ethoxy, pyridin-3-ylmethoxy. 2-hydroxyethoxy, 2- (N, N-dimethylamino) -ethoxy, methoxymethyl, phenoxymethyl, 2-morpholino-4-ylethyl, morpholino-4-ylmethyl, N, N-dimethylaminomethyl, i-propoxy Methyl or phenoxymethyl.

  As used herein, the term “carrier” refers to a relatively non-toxic chemical compound or agent that facilitates the introduction of a compound into cells or tissues.

As used herein, an “EC ₅₀ ” is a specific that indicates a dose-dependent response at 50% of maximum expression of a specific response elicited, caused or enhanced by a specific test compound. Refers to the dose, concentration or amount of a test compound.

  As used herein, “effective amount” refers to the amount of active composition necessary to provide a therapeutic effect to a subject. As used herein, “therapeutically effective amount” refers to the amount of an agent or compound administered that is sufficient to alleviate one or more symptoms of the disease, disorder or condition being treated. To tell. In some embodiments, the result is a reduction and / or alleviation of disease signs, symptoms or causes, or any other desired change in the life system. For example, in some embodiments, an “effective amount” for therapeutic use is disclosed herein as necessary to provide a clinically significant reduction in disease symptoms without undue adverse side effects. The amount of the composition containing the compound. In some embodiments, an appropriate “effective amount” in each case is determined using techniques such as a dose escalation study. The term “therapeutically effective amount” includes, for example, a prophylactically effective amount. In other embodiments, an “effective amount” of a compound disclosed herein, such as a compound of formula (A) or formula (I), may produce a desired pharmacological effect or therapeutic effect without undue adverse side effects. An amount effective to achieve improvement. In other embodiments, an “effective amount” or “therapeutically effective amount” is a variation in metabolism of a compound of formula (A) or formula (I), subject age, weight, general condition, being treated It will be appreciated that it will vary from subject to subject, depending on the condition, the severity of the condition being treated, and the judgment of the attending physician.

In some embodiments, “heterocycloalkyl” is a saturated or unsaturated monovalent cyclic group of 3 to 8 ring atoms, wherein one or two ring atoms are N, O, or A hetero atom selected from S (O) _n (wherein n is an integer of 0 to 2), and the remaining ring atoms are C. In other embodiments, one or two ring carbon atoms are optionally replaced with a -CO- group. In other embodiments, the term heterocycloalkyl includes pyrrolidino, piperidino, morpholino, piperazino, tetrahydropyranyl, tetrahydroquinolinyl and thiomorpholino, and derivatives thereof (where the heterocycloalkyl ring is substituted with the substituents listed below: And N-oxides or protected derivatives thereof, but are not limited to these. Heterocycloalkyl is optionally fused to an aryl. Unless stated otherwise, heterocycloalkyl rings are optionally alkyl, alkoxy, halo, haloalkyl, haloalkoxy, amino, alkylamino, dialkylamino, hydroxy, hydroxyalkyl, hydroxyalkyloxy, hydroxyalkoxyalkyl, alkoxyalkyl. Oxyalkyl, optionally substituted phenyl, optionally substituted phenylalkyl, cycloalkyloxy, cycloalkenyloxy, optionally substituted phenylcarbonylamino, optionally substituted heteroaryl, optionally substituted heteroaralkyl Oxy, aminoalkyl, aminoalkoxy, alkoxyalkyl, alkoxyalkyloxy, methylenedioxy, haloalkoxyalkyl, optionally substituted phenyloxyalkyl, optionally Heteroaryloxyalkyl, optionally substituted heterocycloalkyloxyalkyl, optionally substituted heterocycloalkylalkyl, optionally substituted heterocycloalkylalkyloxy, optionally substituted heterocycloalkyloxy,- Alkylene-S (O) _n -R ^a , wherein n is 0-2, R ^a is alkyl, haloalkyl, hydroxyalkyl, alkoxyalkyl, optionally substituted phenyl, optionally substituted phenyl Alkyl, optionally substituted heteroaryl, or optionally substituted heteroaralkyl), -alkylene-NHSO ₂ -R ^b , where R ^b is alkyl, haloalkyl, optionally substituted phenyl, optionally Substituted phenylalkyl, optionally substituted heteroary Or optionally a heteroaromatic substituted aralkyl), - in the alkylene -NHCO-R c ^(wherein, R ^c is alkyl, haloalkyl, optionally substituted phenyl, optionally substituted phenylalkyl, optionally substituted Or-(alkylene) _n1 -CONR ^d R ^{e where} n1 is 0 or 1, and R ^d and R ^e are independently , Hydrogen, alkyl, haloalkyl, hydroxyalkyl, alkoxyalkyl, aminoalkyl, optionally substituted phenyl, optionally substituted phenylalkyl, optionally substituted heteroaryl, optionally substituted heteroaralkyl, or optionally a substituted heterocycloalkylalkyl, or R ^d and R ^e, Together with the nitrogen atom to which they are attached form a heterocycloalkyl) (wherein the alkyl chain in the haloalkoxyalkyl, optionally substituted phenyloxyalkyl, optionally substituted heteroaryloxyalkyl, Or the aminoalkyl is optionally substituted with 1, 2 or 3 substituents independently selected from 1 or 2 fluoro. In some embodiments, the substituents are independently methoxy, methyl, ethyl, chloro, trifluoromethyl, fluoro, 2-methoxyethoxy, 2- (morpholin-4-yl) ethoxy, pyridin-3-ylmethoxy. 2-hydroxyethoxy, 2- (N, N-dimethylamino) ethoxy, methoxymethyl, phenoxymethyl, 2-morpholino-4-ylethyl, morpholino-4-ylmethyl, N, N-dimethylaminomethyl, i-propoxymethyl Or phenoxymethyl.

In other embodiments, “heteroaryl” is a monovalent monocyclic or bicyclic aromatic radical of 5-10 ring atoms, including one or more (in some embodiments, 1 2 or 3 ring atoms) means a heteroatom selected from N, O or S, the remaining ring atoms being carbon. In a further embodiment, the term heteroaryl includes pyridyl, pyrrolyl, imidazolyl, thienyl, furanyl, indolyl, quinolyl, pyrazinyl, pyrimidinyl, pyridazinyl, oxazolyl, isoxazolyl, benzoxazolyl, benzothiophenyl, benzthiazolyl, quinolinyl, isoquinolinyl, benzofuranyl , Benzopyranyl, and thiazolyl, and derivatives thereof (formed when the heterocycloalkyl ring is substituted with the substituents listed below), or N-oxides, or protected derivatives thereof. Unless stated otherwise, heteroaryl rings are optionally alkyl, alkoxy, halo, haloalkyl, haloalkoxy, amino, alkylamino, dialkylamino, hydroxy, hydroxyalkyl, hydroxyalkyloxy, hydroxyalkoxyalkyl, alkoxyalkyloxy. Alkyl, optionally substituted phenyl, cycloalkyloxy, cycloalkenyloxy, optionally substituted phenylcarbonylamino, optionally substituted heteroaryl, optionally substituted heteroaryloxy, optionally substituted heteroaralkyl Oxy, aminoalkyl, aminoalkoxy, alkoxyalkyl, alkoxyalkyloxy, methylenedioxy, haloalkoxyalkyl, optionally substituted phenylalkyl, optionally substituted Enyloxy, optionally substituted phenylalkyloxy, optionally substituted phenyloxyalkyl, optionally substituted heteroaryloxyalkyl, optionally substituted heterocycloalkyloxyalkyl, optionally substituted heterocycloalkylalkyl , Optionally substituted heterocycloalkylalkyloxy, optionally substituted heterocycloalkyloxy, -alkylene-S (O) _n -R ^a , wherein n is 0-2 and R ^a is Alkyl, hydroxyalkyl, haloalkyl, optionally substituted phenyl, optionally substituted phenylalkyl, optionally substituted heteroaryl, or optionally substituted heteroaralkyl), -alkylene-NHSO ₂ -R ^b (wherein, ^{R b} is alkyl, haloalkyl, optionally Substituted phenyl, optionally substituted phenylalkyl, optionally substituted heteroaryl, optionally substituted heteroaralkyl, or optionally substituted heterocycloalkyl), - alkylene -NHCO-R ^c ( Wherein R ^c is alkyl, haloalkyl, hydroxyl, optionally substituted phenyl, optionally substituted phenylalkyl, optionally substituted heteroaryl, optionally substituted heteroaralkyl, or optionally substituted Is heterocycloalkyl),-(alkylene) _n1- CONR ^d R ^f , where nl is 0 or 1, R ^d is hydrogen or alkyl, and R ^f is hydrogen, alkyl, hydroxylalkyl, Alkoxyalkyl, optionally substituted phenyl, optionally substituted phenylalkyl Is an optionally substituted heteroaryl, an optionally substituted heteroaralkyl, or an optionally substituted heterocycloalkylalkyl, or R ^d and R ^f are taken together with the nitrogen atom to which they are attached. , Heterocycloalkyl, -alkylene-NR ^e -alkylene CONR ^c R ^d , wherein R ^c is as defined above, R ^d and R ^e are independently hydrogen or alkyl, or Form a carboxyalkylaminoalkyl), wherein the alkyl chain in haloalkoxyalkyl, optionally substituted phenyloxyalkyl, optionally substituted heteroaryloxyalkyl, or aminoalkyl is optionally one or 1, 2 or 3 independently selected from (substituted with 2 fluoro) It is substituted with a substituent. In some embodiments, the substituents are independently methoxy, methyl, ethyl, chloro, trifluoromethyl, fluoro, 2-methoxyethoxy, 2- (morpholin-4-yl) ethoxy, pyridin-3-ylmethoxy. 2-hydroxyethoxy, 2- (N, N-dimethylamino) ethoxy, methoxymethyl, phenoxymethyl, 2-morpholino-4-ylethyl, morpholino-4-ylmethyl, N, N-dimethylaminomethyl, i-propoxymethyl Or phenoxymethyl.

  When the heteroaryl ring is divalent, the ring is referred to herein as a heteroarylene.

As used herein, “IC ₅₀ ” refers to the amount, concentration or dose of a particular test compound that achieves 50% inhibition of maximal response in an assay that measures response.

“Isomers” and “multiple isomers” mean compounds of formula (A) or formula (I) that have the same molecular formula but differ in the nature or sequence of bonding of atoms or the arrangement of atoms in space. . Isomers that differ in the arrangement of their atoms in space are termed “stereoisomers”. Stereoisomers that are not mirror images of each other are called “diastereomers”, and stereoisomers that are non-superimposable mirror images are called “enantiomers” and are also called “optical isomers”. An atom bonded to four nonidentical substituents is termed a “chiral center”. A compound with one chiral center is in two opposite chirality enantiomeric forms, and a mixture of the same amount of both enantiomeric forms is called a racemate. Unless a compound is a meso (ie, the compound has two or more asymmetric or chiral centers, but is not chiral because it contains an internal symmetry plane), a compound having one or more chiral centers is 2 ^{n -1} (where n is the number of chiral centers) enantiomeric pairs (including plural). In some embodiments, a compound having multiple chiral centers exists as either a single diastereomer or as a mixture of diastereomers, referred to as a “diastereomeric mixture”. In some other embodiments, if one chiral center is present, the stereoisomer is characterized by the absolute configuration of that chiral center. Absolute configuration refers to the arrangement in space of the substituents attached to the chiral center. Enantiomers are characterized by the absolute configuration of their chiral centers and are described by Cahn-Ingold and Prelog R- and S-ranking rules. Stereochemical nomenclature, stereoisomer stereochemistry and methods for determining separation are well known in the art (eg, “Advanced Organic Chemistry”, Volume 4, March, Jerry, John Wiley & Sons, New York, 1992). To describe the compounds of formula (A) or formula (I), the names and figures used in this application include all possible stereoisomers and any mixtures, their racemates, etc. It is understood that

  Also described herein are prodrugs of compounds of formula (A) or formula (I). The term prodrug refers to a covalently bonded carrier that can release an active ingredient of formula (A) or formula (I) when the prodrug is administered to a mammalian subject. Release of the active ingredient occurs in vivo. In some embodiments, the method of preparing a prodrug generally modifies the proper functional group in a compound. However, these modified functional groups regenerate back to the original functional groups in normal operation or in vivo. Examples of the prodrug of the compound of formula (A) or formula (I) include compounds in which a hydroxy group, an amino group, a carboxyl group or a similar group is modified. Examples of prodrugs include esters (eg, acetate, formate and benzoate derivatives), carbamates (eg, N or N of hydroxy or amino functional groups in compounds of formula (A) or formula (I), N-dimethylaminocarbonyl), amides (for example, trifluoroacetylamino, acetylamino, etc.) and the like, but are not limited thereto.

  Also described herein are N-oxide derivatives and protected derivatives of compounds of formula (A) or formula (I). For example, in some embodiments, when the compound of formula (A) or formula (I) contains an oxidizing nitrogen atom, the nitrogen atom is converted to an N-oxide by known methods. In other embodiments, when the compound of formula (A) or formula (I) comprises any group comprising a group, such as a hydroxy, carboxy, thiol, or nitrogen atom (s), these groups are: Protected with a suitable protecting group. A comprehensive list of suitable protecting groups can be found in T.W. W. Greene, Protective Groups in Organic Synthesis, John Wiley & Sons, Inc. Appropriate list of protecting groups, which can be found in 1981, is hereby incorporated by reference. In other embodiments, protected derivatives of compounds of formula (A) or formula (I) are produced by known methods.

  "Pharmaceutically acceptable derivatives" as pharmaceutically acceptable salts, pharmaceutically acceptable N-oxides, pharmaceutically active metabolites, pharmaceutically acceptable prodrugs, pharmaceutically acceptable Solvates, and pharmaceutically acceptable esters, but are not limited to these.

  “Pharmaceutically acceptable salt” of a compound means a salt that is pharmaceutically acceptable and that possesses the desired pharmacological activity of the parent compound. As such salts, inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, etc., or acetic acid, propionic acid, hexanoic acid, cyclopentanepropionic acid, glycolic acid, pyruvic acid, lactic acid, malonic acid , Succinic acid, malic acid, maleic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, 3- (4-hydroxybenzoyl) benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, 1,2 -Ethanedisulfonic acid, 2-hydroxyethanesulfonic acid, benzenesulfonic acid, 4-chlorobenzenesulfonic acid, 2-naphthalenesulfonic acid, 4-toluenesulfonic acid, camphorsulfonic acid, glucoheptonic acid, 4,4'-methylenebis- (3 -Hydroxy-2-ene-1-carboxylic acid), 3-phenylpropionic acid, trimethylacetic acid, Acid addition salts formed with organic acids such as tributylacetic acid, laurylsulfuric acid, gluconic acid, glutamic acid, hydroxynaphthoic acid, salicylic acid, stearic acid, muconic acid, etc., or acidic protons present in the parent compound become metal ions Coordination with organic bases such as, for example, salts formed when replaced by alkali metal ions, alkaline earth metal ions or aluminum ions, or ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, etc. Is mentioned. It is understood that pharmaceutically acceptable salts are non-toxic. Additional information regarding suitable pharmaceutically acceptable salts can be found in Remington's Pharmaceutical Sciences, 17th edition, Mack Publishing Company, Easton, Pa. 1985 (list of pharmaceutically acceptable salts), which is incorporated herein by reference.

  A “pharmaceutically acceptable carrier or excipient” is a carrier or excipient that is useful in preparing a pharmaceutical composition and is generally safe, non-toxic, biologically or otherwise undesirable. By excipients is meant including carriers or excipients that are acceptable for veterinary use and human pharmaceutical use. In some embodiments, a “pharmaceutically acceptable carrier / excipient” as used herein and in the claims includes both one of the excipients and a plurality of the excipients. .

  In other embodiments, the compounds of Formula (A) or Formula (I) have asymmetric centers. In other embodiments, compounds of Formula (A) or Formula (I) that contain asymmetrically substituted atoms are isolated in optically active forms or racemates. All chiral, diastereomeric, and racemic forms are described herein unless a specific stereochemistry or isomeric form is specifically indicated.

  In some embodiments, certain compounds of formula (A) or formula (I) exist as tautomers and / or geometric isomers. All possible tautomers, as well as cis and trans-isomers, alone and mixtures thereof are also of interest. Furthermore, the term alkyl as used herein, although only a few examples are mentioned, includes all possible isomeric forms of the alkyl group. Furthermore, when cyclic groups such as aryl, heteroaryl, heterocycloalkyl are substituted, only a few examples are given, but they include all positional isomers. Furthermore, polymorphic forms and hydrates of the compounds of formula (A) or formula (I) are also of interest.

  When modifying a particular group, “optionally substituted” means that the group that the term modifies may be substituted, but need not be substituted. Where the term “optionally substituted” is used to modify a particular group, unless stated otherwise, this means that any other group not so modified is optionally substituted Does not mean there is no possibility of being. Further, when a group is defined as being substituted by one of a number of listed optional substituents, the group may be substituted with one or more unlisted substituents unless otherwise stated. It does not mean that there is no possibility of further substitution with groups. For example, “optionally substituted heterocycloalkyl” means that the heterocycloalkyl is substituted with the substituents listed within the definition of “optionally substituted heterocycloalkyl” Means that it is not necessary, and the description includes situations in which the heterocycloalkyl group is substituted and situations in which the heterocycloalkyl group is not substituted.

  “Optionally substituted phenyl” is optionally alkyl, halo, alkoxy, alkylthio, haloalkyl, haloalkoxy, heteroaryl (optionally from alkyl, halo, hydroxy, alkoxy, carboxy, amino, alkylamino or dialkylamino). Independently substituted with one or two independently selected substituents), heterocycloalkyl (optionally selected from alkyl, halo, hydroxy, alkoxy, carboxy, amino, alkylamino or dialkylamino) Substituted by 1 or 2 substituents), amino, alkylamino, dialkylamino, hydroxy, cyano, nitro, methylenedioxy, aminocarbonyl, acylamino, hydroxyalkyl, alkoxycarbonyl, aminoalkyl, or It means that one independently selected from carboxy, substituted with two or three substituents, or optionally five phenyl ring substituted with a fluorine atom. When phenyl is substituted, it is referred to herein as “substituted phenyl”.

  In some embodiments, “optionally substituted heteroaryl” is a monovalent monocyclic or bicyclic aromatic radical of 5 to 10 ring atoms, and includes one or more (some In embodiments, 1, 2 or 3 ring atoms) are heteroatoms selected from N, O or S and the remaining ring atoms are carbon, which carbon is optionally alkyl, Halo, alkoxy, haloalkyl, haloalkoxy, amino, alkylamino, dialkylamino, hydroxy, cyano, nitro, aminocarbonyl, hydroxyalkyl, alkoxycarbonyl, aminoalkyl, optionally substituted phenyl, optionally substituted phenoxy, carboxy Or heteroaryl, which is optionally alkyl, halo, hydroxy, alkoxy, carboxy, amino, alkyl Substituted with 1 or 2 substituents, optionally substituted with 1 or 2 substituents independently substituted with alkyl, halo, hydroxy, alkoxy, amino, alkylamino or dialkylamino; Or heterocycloalkylalkyl, optionally substituted with one or two substituents independently selected from alkyl, halo, hydroxy, alkoxy, amino, alkylamino or dialkylamino, optionally alkyl, halo, hydroxy, With one, two or three substituents independently selected from heteroarylamino substituted with one or two substituents independently selected from alkoxy, amino, alkylamino or dialkylamino Means a substituted radical. More specifically, the term optionally substituted heteroaryl includes pyridyl, pyrrolyl, imidazolyl, thienyl, furanyl, indolyl, quinolyl, pyrazinyl, pyrimidinyl, pyridazinyl, oxazolyl, isoxazolyl, benzoxazolyl, quinolinyl, isoquinolinyl, Examples include, but are not limited to, benzopyranyl and thiazolyl, and derivatives thereof (formed when the heteroaryl ring is substituted with the substituents listed above), or N-oxides or protected derivatives thereof.

In a further embodiment, “optionally substituted heterocycloalkyl” is a saturated or unsaturated monovalent cyclic group of 3 to 8 ring atoms, wherein one or two ring atoms are N , O or S (O) _n (wherein n is an integer from 0 to 2), and the remaining ring atoms are C. In another embodiment, one or two ring carbon atoms are optionally replaced with a -CO- group. In other embodiments, the term heterocycloalkyl is pyrrolidino, piperidino, morpholino, piperazino, tetrahydropyranyl and thiomorpholino, and derivatives thereof (formed when the heterocycloalkyl ring is substituted with the substituents listed below. ), Or N-oxides or protected derivatives thereof, but are not limited thereto. Heterocycloalkyl is optionally fused to aryl and is optionally substituted with alkyl, cycloalkyl, halo, alkoxy, haloalkyl, haloalkoxy, amino, alkylamino, dialkylamino, hydroxy, cyano, nitro, optionally substituted Substituted with one, two or three substituents independently selected from phenylalkyl, optionally substituted heteroaralkyl, aminocarbonyl, hydroxyalkyl, alkoxycarbonyl, aminoalkyl or carboxy.

  “RNAi” or “RNA interference” refers to the introduction of homologous double-stranded RNA (dsRNA) that specifically targets gene transcripts, resulting in zero or low trait levels. The RNAi method is highly sequence specific, very sensitive and requires only a few dsRNA molecules per cell for effective interference.

In some embodiments, “treating” or “treatment” of a disease, disorder, or condition includes at least in part:
(1) Preventing a disease, disorder or condition, ie, preventing clinical manifestations of a disease, disorder or condition in a mammal, ie, being exposed to or susceptible to a disease, disorder or condition Have not yet experienced or manifested symptoms of the disease, disorder or condition,
(2) inhibiting a disease, disorder or condition, ie inhibiting or reducing the progression of the disease, disorder or condition, or its clinical symptoms, or (3) alleviating the disease, disorder or condition, ie Cause regression of the disease, disorder or condition, or its clinical symptoms.

  The term “treating cancer” or “treatment of cancer” refers to administration to a mammal suffering from a cancer condition and refers to the effect of reducing the cancer condition by killing the cancer cells, but the growth of the cancer and Also referred to as a result of metastasis inhibition.

For convenience only, unless otherwise stated, the term “formula (A) or formula (I)” is used to refer to formula (A), formula (I), formula (a), formula (b), formula (c) ), Any compound having the structure of formula (d), formula (e), compounds of any specific embodiments described herein, and any of the general formulas described above It is used as an abbreviation for any specific compound described herein.
Homologous recombination and DNA repair

  In the middle of many physiological events, as well as in response to various environmental disorders, cellular DNA undergoes double-strand breaks (DSB). In some cases, if left unrepaired, such DSBs cause mutations that have proven to be fatal to the organ. In human cells, DNA DSB repair occurs by either homologous recombination (HR) or non-homologous end joining (NHEJ). Homologous recombination is known to involve RAD51, RAD52, RAD54, RAD55-57 and RPA protein. More recently, BRCA1 and BRCA2 cancer susceptibility proteins have also been suggested to play a role in homologous DSBR repair through interaction with RAD50 and RAD51. RAD51 is thought to be a stably bound core component of the multiprotein HR-repair complex at the site of DNA damage, and binding proteins such as RAD52 and RAD54 interact rapidly and reversibly with the focal RAD51 DNA repair complex. It is suggested to work.

  Homologous recombination is an essential process that is important for maintaining the integrity of the genome. In E. coli, RecA protein plays a central role in homologous genetic recombination in vivo, and in vitro double-stranded DNA homology with single-stranded DNA or partially single-stranded DNA molecules. Promote pairing. In the yeast Saccharomyces cerevisiae, there are several genes that have homology to the RecA gene, ie, RAD51, RAD57, and DMCl. All members of the RAD51 family and their bacterial equivalents (RecA) share an important structural motif known as the “RecA signature sequence” (also referred to as the “homologous core region” or domain II). This sequence forms an ATP binding site that is an important property of all these proteins. However, the eukaryotic members of the RAD51 family are bacterial due to the presence of an N-terminal extension that exists only in the RAD51 family member and a C-terminal extension of about 100 amino acids that is present in RecA but not in the RAD51 family member. It can be distinguished from sex RecA protein. All known members of the RAD52 epistasis group are required for DSB repair and genetic recombination. Functional analysis reveals the interaction of RAD57 with RAD51, RAD52 and RAD55 to form “recombinosomes” (Johnson, R. et al., 1995, MoI. Cell. Biol. 15: 4843 4850).

  Many beneficial and lifesaving chemotherapeutic drugs are actively used in the clinic and have listed their effects by damaging DMA in proliferating cells. Such chemotherapeutic agents include, for example: (1) alkylating agents such as temozolomide, salmustine, chlorambucil, melphalan, dacarbazine, BCNU and SCNU, (2) nucleoside analogs such as fludarabine, iodouridine Deoxyribose, gemcitabine and fluorodeoxyuridine, and (3) radiation therapy. These therapies cause cytotoxic modifications at the DNA base, which initially cause single-strand breaks (SSB) in the DNA strand into which the drug is introduced as well as in the complementary complementary strand DNA. These SSBs subsequently increase the amount of DSB, leading to cell death if not repaired correctly.

In some embodiments, if the cells are resistant to certain DNA damaging agents, various radioactive and chemical sensitizers are used to increase sensitivity to these DNA damaging agents. Proliferating tumors or virus-infected cells are often resistant to chemotherapy and radiation therapy due to overexpression of DNA repair mechanisms. Since SSB can be converted to DSB, even if one of these pathways is blocked, the other pathway repairs cell damage and maintains viability. In some embodiments, an agent that inhibits DNA repair in a specific and potent manner sensitizes proliferating cells to a broad spectrum anticancer agent. Since cancer cells allow for rapid growth through DNA repair, this sensitization allows for the specificity of cancer treatment and is a more effective treatment with lower side effects than can occur with current treatment regimens. May be possible.
RAD51 and RAD51 inhibitor

  RAD51, a eukaryotic recombinase and a homologue of the bacterial RecA protein involved in homologous recombination catalyze double strand break repair (DSBR) in damaged cells. RAD51 is a member of the RAD52 epistasis group, which includes RAD50, RAD51, RAD52, RAD54, RAD55 and RAD57. In some embodiments, a method provided herein comprises a group consisting of RAD52 epistasis group protein, RAD51, RAD52, RAD54, RAD55, MRE1 and XRS2, mismatch repair group protein PMSL, and nucleotide excision repair group protein RAD10. Alter the expression or activity of at least one protein selected from According to phylogenetic analysis by Ogawa and co-workers, two subfamilies within the eukaryotic RecA homologue, namely RAD51-like genes (human, mouse, chicken, S. cerevisiae, S. pombe RAD51 and acapangabi Mei3 ) And DMCl-like genes (S. cerevisiae DMCl and Lily LIM15).

  RAD51 protein is important for repair of DSB in damaged cells. S. In S. cerevisiae, RAD51, RAD57 and DMC1 are mentioned as genes having homology to RecA. RAD51 is highly overexpressed in certain tumor cells and its activity is down-regulated, resulting in inhibition of DSB repair. RAD51 protein plays a central role in gene conversion during homologous recombination induced by ionizing radiation (IR) or ultraviolet (UV) irradiation, DNA damaging agents, and replication extenders, and sister chromosome exchange ( It plays a role in SCB). In further embodiments, increased expression levels of E. coli RecA or RAD51 increase cellular resistance to radiation or other DNA damaging agents.

  In one embodiment, RAD51 comprises a homologue of RAD51. In one embodiment, a RAD51 homologue is defined by the role of RAD51 in recombination repair. In another embodiment, the RAD51 homologue is significantly different from E. coli RecA protein of 33-240 residues (which is a “RecA signature sequence” or “homologous core region” as described above). Proteins that share common sequence identity. RAD51 homologues include RecA and RAD51 homologues in yeast and mammals (see above). In another embodiment, RAD51 is a dimer. In a further embodiment, the dimer is a homodimer or a heterodimer. In some embodiments, the heterodimer is formed from two different homologues. In one embodiment, the homologue is selected from the group consisting of RAD51A, RAD51B, RAD51C and RAD51D. In some embodiments, the dimer comprises RAD51C or RAD51B in any combination.

  In a further embodiment, the level of RAD51 expression is measured by the level of RAD51 protein or nucleic acid. In some embodiments, a labeled binding agent that binds to RAD51 is used to detect RAD51 protein. As used herein, the term “labeled” refers to a compound having at least one element, isotope or chemical compound attached to allow detection of the compound. In some embodiments, the label is in three forms: (1) an isotope label that is a radioisotope or heavy isotope, (2) an immunolabel that is an antibody or antigen, and (3) a colored dye or fluorescent dye. being classified. In another embodiment, the binding agent is directly labeled or indirectly labeled by using a labeled second agent that binds to the first binding agent. In one embodiment, the level is determined by using a polyclonal antibody. In some embodiments, the level is determined by using a monoclonal antibody. In some embodiments, the antibody is raised against eukaryotic RAD51. In some embodiments, the eukaryotic RAD51 is a mammalian RAD51. In another embodiment, antibodies are raised against RAD51 homologues. In a further embodiment, RAD51 expression is determined in the same manner as described above by the level of RAD51 nucleic acid, such as mRNA.

  The “biological activity” of RAD51 in the present specification includes RAD51 DNA-dependent ATPase activity, nucleic acid strand exchange activity, lesion formation, single- and double-strand binding activity, filament formation (with yeast RecA filament and The same), pairing activity (D-loop formation), etc., but are not limited thereto.

  In another embodiment, as used herein, inhibition of RAD51 biological or biochemical activity comprises: DNA-dependent ATPase activity, RAD51 foci formation, nucleic acid strand exchange, DNA binding, nucleoprotein filaments Measured from RAD51 activity selected from the group consisting of formation, DNA pairing and DNA repair. DNA repair and recombination are generally considered biological activities of RAD51. In further embodiments, the DNA repair is double-strand break repair, single-strand annealing, or post-replication recombinant repair.

  As used herein, a RAD51 inhibitor or an agent or composition having RAD51 inhibitory activity has at least about 30%, at least about 40%, at least about 50% expression or translation of a RAD51 nucleic acid, or biological activity of a RAD51 peptide. %, At least about 70%, at least about 90%, and at least about 95%. In one embodiment, a RAD51 inhibitor, such as a compound having the structure of formula (A) or formula (I), inhibits RAD51 nucleic acid expression or translation, or RAD51 protein activity by at least about 70%. In another embodiment, inhibition of RAD51 activity is defined as a detectable decrease in RAD51 activity compared to a control without a RAD51 inhibitor.

One aspect is a method of treating cancer comprising:
(A) in a patient suffering from cancer, inhibiting the activity of at least one therapeutically effective amount of RAD51, preventing the formation of RAD51 foci, or of a functional repair complex for homologous recombination of DNA Administering drugs that interfere with construction;
(B) administering to the patient a treatment capable of damaging cellular DNA;
It is a method including.

  In one embodiment, at least one cancer cell from the patient has a defect in non-homologous end joining of DNA.

  One aspect is a method of treating a disease, disorder or condition associated with a deficiency in non-homologous end joining of DNA, comprising: (a) a human suffering from a disease, disorder or condition associated with a deficiency in non-homologous end joining of DNA Administering to a patient an agent that inhibits the activity of at least one therapeutically effective amount of RAD51, prevents the formation of RAD51 foci, or prevents the construction of a functional repair complex for homologous recombination of DNA And (b) administering to the human patient a therapeutically effective amount of a DNA damaging agent. In a further embodiment, the DNA damaging agent is doxorubicin. In one embodiment, the agent that inhibits the activity of at least one RAD51, prevents the formation of RAD51 foci, or prevents the construction of a functional repair complex for homologous recombination of DNA is at least one histone Deacetylase inhibitor. In another embodiment, the administration of at least one histone deacetylase inhibitor and doxorubicin are administered simultaneously. In a further embodiment, the administration of at least one histone deacetylase inhibitor and doxorubicin has a synergistic effect. In another embodiment, the effect is compatible. In yet a further embodiment, the disease, disorder, or condition is non-Hodgkin lymphoma.

  Also, RAD51 inhibitors include RAD51 peptide inhibitors (including RAD51 antibodies including but not limited to 94-160 and 264-315 amino acids p53, and single chain antibodies), small molecules, nucleotide analogs (Including but not limited to ADP analogs, ATPγS), minor groove DNA binding agents (including but not limited to distamycin and its derivatives) as inhibitors of RAD51, known in the biochemical activity of RAD51 Examples include, but are not limited to, radiation sensitizers (eg, xanthine derivatives including xanthine and caffeine), antibodies to RAD51, particularly antigens that inhibit transcription by immobilized hybrids, and antisense molecules. In another embodiment, the inhibitor inhibits RAD51 directly or indirectly by interacting with at least a portion of a RAD51 nucleic acid, RAD51 mRNA, or RAD51 protein. Further, the inhibitors herein are utilized alone or in combination with each other.

  In a further embodiment, RAD51 inhibitors, such as compounds having the structure of formula (A) or formula (I), include inhibitors of RAD51 homologs, including RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3 As well as other RecA homologues (see above).

  In a further embodiment, in cultured human cells, RAD51 protein is detected in multiple discrete lesions within the nucleus by immunofluorescent antibodies. After DNA damage, the localization of RAD51 changes dramatically when multiple foci form in the nucleus and are vividly stained with anti-RAD51 antibodies. Normally, cells with locally enriched RAD51 protein increase after DNA damage show unscheduled DNA repair synthesis. Two main types of RAD51 lesions have been identified, and by in situ immunostaining with RAD51 antibody, (1) nuclei that did not show any staining state (no lesions), (2) weak to moderate staining Three types of nuclei were revealed: nuclei that showed status and showed only some lesions (type I nuclei), and (3) nuclei that showed strong staining and showed many lesions (type II nuclei) ing. In normal cells, type I nuclei are usually found in 7-10% of the cells, type II nuclei are found in less than 0.4-1% of the cells, and generally about 90% of the cells show no foci. . In contrast, some cells involved in disease states show a marked increase in RAD51 foci.

  RAD51 foci are determined in various ways. In some embodiments, a labeled binding agent that binds to RAD51 is used to visualize the lesion. In one embodiment, the label is incorporated into the binding agent at any position. In some embodiments, the label is a fluorescent or radioactive label. In another embodiment, the binding agent is labeled directly, or indirectly by using a labeled second agent that binds to the first binding agent. Cell or tissue samples are prepared using standard techniques, as known for cell or in situ staining.

In some embodiments, the binding agent used to detect RAD51 foci is an antibody. In one embodiment, the antibody is either polyclonal or monoclonal. In some embodiments, an antibody under evaluation against a particular RAD51 is used, ie, an antibody against human RAD51 is used in an evaluation of a human patient. However, the homology between different mammalian RAD51 molecules is very high (eg, 73% identity between humans and chickens), so to evaluate different animals, antibodies against RAD51 can be obtained from one animal. It can be used (such as a mouse antibody for evaluating human tissue). Thus, in some embodiments, antibodies made against eukaryotic RAD51 are used. In some embodiments, the eukaryotic RAD51 is a mammalian RAD51. Thus, in some embodiments, antibodies made against the yeast, human, rodent, primate, and avian RAD51 proteins are used. Furthermore, the protein used to produce the antibody need not be a full-length protein. In some embodiments, fragments and derivatives are used as long as there is sufficient immunoreactivity for sample RAD51 to detect. In another embodiment, other binding agents that bind to RAD51 with sufficient affinity for visualization are used.
Selection of RAD51 mRNA / protein patients

  One aspect is a method of selecting a cancer treatment for a patient in need of cancer treatment, a) determining the expression level of RAD51 mRNA or the level of RAD51 protein in at least one cancer cell from the patient. And b) when the RAD51 mRNA expression level or RAD51 protein level in the biological sample is higher than the RAD51 mRNA expression level or RAD51 protein level in the standard sample, at least one histone deacetylase inhibitor is effective for treatment. Suggesting that it is the target. In one embodiment, the method comprises determining the expression level of RAD51 mRNA in at least one cancer cell from the patient. In another embodiment, the method comprises determining the level of RAD51 protein in at least one cancer cell from the patient. One embodiment is a method wherein suggesting includes providing a result that at least one histone deacetylase inhibitor is likely to be therapeutically effective. Another embodiment is a method wherein suggesting includes providing a result that at least one histone deacetylase inhibitor is likely to respond to treatment. In yet another embodiment, the method further comprises administering a therapeutically effective amount of at least one histone deacetylase inhibitor. In still further embodiments, the at least one histone deacetylase inhibitor is selected from compounds of formula (A) or (I). In another embodiment, the at least one histone deacetylase inhibitor is selected from compounds of formula (A), (B), (C) and / or (D). In yet another embodiment, the at least one histone deacetylase inhibitor is 3-((dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide. It is. In one embodiment, the standard sample is an HH skin T-cell lymphoma cell line. In another embodiment, the level of RAD51 protein in the standard sample is a reference level in an HH skin T-cell lymphoma cell line. In another embodiment, the level of RAD51 protein in the standard sample is at least about 50%, at least about 60%, at least about 70%, at least about 75%, at least about 80%, at least about at least about the level of RAD51 protein in the biological sample. 90%, about 100%. In another embodiment, the level of RAD51 protein in the standard sample is at least about 11/2 times, at least about 2 times, at least about 3 times, at least about 4 times, at least about 5 times the level of RAD51 in the biological sample. At least about 6 times, at least about 7 times, at least about 8 times, at least about 9 times, at least about 10 times, at least about 12 times, at least about 15 times, or at least about 20 times. In a further embodiment, the standard sample is normalized to the internal protein. In still further embodiments, the internal protein is actin. In one embodiment, normalization of the standard sample is measured by Western blot. In another embodiment, the standard sample correlates with the% level of apoptosis in vitro. In a further embodiment, the percent level of apoptosis is less than about 20%. In still further embodiments, the percent level of apoptosis is below about 15%. In another embodiment, the percent level of apoptosis is below about 10%. In a further embodiment, the percent level of apoptosis is below about 5%.

In one embodiment, the method of selecting a patient in need of treatment further comprises formulating or administering at least one histone deacetylase inhibitor based on the results of the suggesting step. In one embodiment, the expression level of RAD51 mRNA or the level of RAD51 protein in a biological sample is determined by standard immunodetection methods (eg, Western blot analysis, radioimmunoassay, or ELISA).
BRCA1 and BRCA1 modulators

  BRCA1 is a human gene that belongs to a class of genes known as tumor suppressors that maintain genomic integrity to prevent uncontrolled growth. The multifactor BRCA1 protein functions in DNA damage repair, ubiquitination, transcriptional control and other processes. Variations in genes are associated with a number of genetic cancers, so-called breast cancer, ovarian cancer and prostate cancer. BRCA1 protein is directly involved in the repair of damaged DNA.

  For many types of nuclei in normal cells, the BRCA1 protein is thought to interact with RAD51 and repair breaks in DNA. These breaks can occur by natural radiation or other exposures, but can also occur when chromosomes transform genetic material in preparation for cell division. A BRCA2 protein having a function similar to that of BRCA1 also interacts with the protein.

  In some embodiments, the methods provided herein inhibit BRCA1 expression or activity. In one embodiment, a BRCA1 inhibitor or agent, or a composition having BRCA1 inhibitory activity, wherein a BRCA1 mRNA or protein level is at least about 30%, about 40%, about 50%, about 70%, It is defined as an agent or composition that reduces about 90% and about 95%. In one embodiment, the BRCA1 inhibitor has a structure of formula (A) or formula (I) and inhibits BRCA1 nucleic acid expression or translation, or BRCA1 protein activity by at least about 70%. In another embodiment, the inhibition of BRCA1 activity is defined as a detectable decrease compared to a sample that has not been exposed to a BRCA1 inhibitor.

One aspect is a method of treating cancer comprising:
(A) Functionally for homologous recombination that inhibits the activity of at least one therapeutically effective amount of BRCA1, prevents the interaction of BRCA1 and RAD51, or involves BRCA1 in patients suffering from cancer Administering an agent that interferes with the construction of the repair complex;
(B) administering to the patient a treatment capable of damaging cellular DNA;
It is a method including.

  In one embodiment, at least one cancer cell from the patient has a defect in non-homologous end joining of DNA.

  BRCA1 is related to the upward control of RAD51. Thus, in some embodiments herein, a method of treating a disease (eg, cancer), disorder or condition comprising: a) administering a BRCA1 inhibitor; and b) the BRCA1 inhibitor inhibits RAD51. Administering a treatment capable of damaging down-regulating cellular DNA. In one embodiment, the BRCA1 inhibitor is a histone deacetylase inhibitor as described herein. In another embodiment, the inhibitor inhibits BRCA1 directly or indirectly by interacting with at least a portion of a BRCA1 nucleic acid, BRCA1 mRNA, or BRCA1 protein. In other embodiments, the inhibitors herein are utilized alone or in combination with each other.

  One embodiment is a method of treating a disease, disorder or condition, wherein the at least one histone deacetylase inhibitor interacts with a DNA repair mechanism involving BRCA1.

  In another embodiment, a method of treating a disease, disorder or condition in a patient where BRCA1 is associated with double-stranded DNA repair, comprising: a) providing the patient with a therapeutically effective amount of at least one BRCA1. Administering an agent that modulates the activity of b) and b) administering to the patient a treatment capable of damaging cellular DNA. Another embodiment is the method wherein the modulation is inhibition of BRCA1 activity.

  In one embodiment, the agent that modulates the activity of at least one BRCA1 is at least one histone deacetylase inhibitor, or a pharmaceutically acceptable derivative thereof. In another embodiment, the agent that modulates the activity of at least one BRCA1 inhibits the activity of BRCA1. In further embodiments, the agent that modulates the activity of at least one BRCA1 reduces cellular levels of BRCA1. In another embodiment, the activity of BRCA1 upregulates RAD51. In yet another embodiment, the agent that modulates the activity of at least one BRCA1 inhibits the activity of RAD51. In a further embodiment, the agent that modulates the activity of at least one BRCA1 reduces cellular levels of RAD51. In another embodiment, the disease, disorder or condition is cancer. In a further embodiment, the cancer is breast cancer, ovarian cancer or prostate cancer. In one embodiment, a treatment capable of damaging cellular DNA is administered when the expression of BRCA1 is within a predetermined range. In yet a further embodiment, the histone deacetylase inhibitor is from about 0.2 mg to about 2000 mg. In another embodiment, the at least one histone deacetylase inhibitor is about 0.2 mg to about 1000 mg, about 1 mg to about 200 mg, about 5 mg to about 100 mg, about 5 to about 50 mg, and about 5 to about 20 mg. It is. In another embodiment, the patient is a human.

One aspect is a method of treating a disease, disorder or condition associated with a deficiency in non-homologous end joining of DNA, a) for a patient suffering from a disease, disorder or condition associated with a deficiency in non-homologous end joining of DNA. Modulate the activity of at least one therapeutically effective amount of BRCA1, prevent the interaction of BRCA1 and RAD51, or prevent the construction of a functional repair complex for homologous recombination involving BRCA1 Administering a drug; and b) administering to the patient a treatment capable of damaging cellular DNA. In another embodiment, the at least one agent modulates the activity of BRCA1. In another embodiment, the at least one agent prevents BRCA1 and RAD51 interaction. In a further embodiment, the at least one agent prevents the construction of a functional repair complex for homologous recombination involving BRCA1. In a further embodiment, the at least one agent is at least one histone deacetylase inhibitor. In yet a further embodiment, the at least one histone deacetylase inhibitor is of the formula (A):
(Where
Q is optionally substituted C _5-12 aryl, or optionally substituted C _5-12 heteroaryl,
L is a linker having at least 4 atoms;
R ¹ is H or alkyl)
And a pharmaceutically acceptable salt thereof, a pharmaceutically acceptable N-oxide, a pharmaceutically active metabolite, a pharmaceutically acceptable prodrug, and a pharmaceutically acceptable solvent. It is a Japanese product. In another embodiment, the histone deacetylase inhibitor has the formula (I):
(Where
R ¹ is hydrogen or alkyl;
X is —O—, —NR ² —, or —S (O) _n , wherein n is 0-2 and R ² is hydrogen or alkyl;
Y is alkylene optionally substituted with cycloalkyl, optionally substituted phenyl, alkylthio, alkylsulfinyl, alkylsulfonyl, optionally substituted phenylalkylthio, optionally substituted phenylalkylsulfonyl, hydroxy, or optionally Substituted phenoxy,
Ar ¹ is phenylene or heteroarylene, wherein said Ar ¹ is optionally one or two groups independently selected from alkyl, halo, hydroxy, alkoxy, haloalkoxy, or haloalkyl Replaced by
R ³ is hydrogen, alkyl, hydroxyalkyl, or optionally substituted phenyl, and Ar ² is aryl, aralkyl, aralkenyl, heteroaryl, heteroaralkyl, heteroaralkenyl, cycloalkyl, cycloalkylalkyl, Heterocycloalkyl or heterocycloalkylalkyl. )
And a single stereoisomer, a single geometric isomer or a mixture thereof, or a pharmaceutically acceptable salt thereof.

  In another embodiment, the histone deacetylase inhibitor has the structure of a compound of formula (A), (B), (C) or (D), or a pharmaceutically acceptable salt thereof. In a further embodiment, the histone deacetylase inhibitor is 3-((dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide.

One aspect is a method of treating a disease, disorder or condition that involves overexpression of homologous recombination of DNA or that involves homologous recombination of DNA as the etiology, comprising: a) homologous recombination of DNA BRCA1 which modulates the activity of a therapeutically effective amount of at least one BRCA1 in a patient suffering from a disease, disorder or condition associated with overexpression of or associated with the homologous recombination of DNA Administering an agent that interferes with the interaction of RAD51 or prevents the construction of a functional repair complex for homologous recombination involving BRCA1, and b) a treatment capable of damaging cellular DNA to the patient Administering
Is a method that includes

  In another embodiment, the agent prevents the construction of a functional repair complex for homologous recombination of DNA. In another embodiment, an agent that modulates the activity of BRCA1 reduces the cellular level of BRCA1.

  In another embodiment, the agent that prevents the construction of a functional repair complex for homologous recombination of DNA is a therapeutically effective amount of at least one histone deacetylase inhibitor, or pharmaceutical agent thereof Is an acceptable derivative. In another embodiment, the disease, disorder or condition is cancer. In another embodiment, the disease, disorder or condition is breast cancer, ovarian cancer or prostate cancer. In another embodiment, the DNA damaging agent is administered when the expression of BRCA1 is within a predetermined range. In another embodiment, the therapeutically effective amount of at least one histone deacetylase inhibitor is about 0.2 mg to about 2000 mg.

In another embodiment, the treatment capable of damaging cellular DNA comprises radiotherapy or administration of a pharmaceutically effective amount of at least one anticancer agent, a known combination scheme of cancer treatment, or any combination thereof. Including. In another embodiment, a treatment capable of damaging cellular DNA comprises radiotherapy or a pharmaceutically effective amount of a topoisomerase inhibitor, tubulin interactor, DNA interacting agent, DNA alkylating agent, and platinum complex. Administration of at least one drug selected from the group consisting of the body. In another embodiment, the treatment capable of damaging cellular DNA includes radiation therapy.
In another embodiment, the anticancer agent is a cytotoxic / cytostatic agent, an antiproliferative agent, a prenylprotein transferase inhibitor, an HMG-CoA reductase inhibitor, a nitrogen mustard, a nitrosourea, an angiogenesis inhibitor, a cell Inhibitors of proliferation and survival signaling pathways, apoptosis-inducing agents, agents that interfere with cell cycle checkpoints, biphosphonates, or any combination thereof.
HDAC and HDAC inhibitors

  In eukaryotic cells, genomic DNA in chromatin binds to histones and forms nucleosomes. Each nucleosome consists of a protein octamer composed of two copies of each of histones H2A, H2B, H3 and H4. DNA is a basic amino acid of histone that interacts with the negatively charged phosphate group of DNA and wraps around the core of this protein. The most common post-translational modification of these core histones is the reversible acetylation of the ε-amino group of a conserved, strongly basic N-terminal lysine residue. Histone reversible acetylation is a major regulator of gene expression that acts by altering the accessibility of transcription factors to DNA. In normal cells, histone deacetylase (HDAC) and histone acetyltransferase (HAT) together control and balance the level of histone acetylation. Inhibition of HDAC results in the accumulation of highly acetylated histones and causes various cellular responses.

Histone acetylation and deacetylation have long been linked to transcriptional control. In some embodiments, HDAC inhibitors, including trichostatin A, sodium butyrate, suberoylanilide hydroxamic acid (SAHA), depsipeptide, MS-275 and aphicidin, promote histone acetylation and chromatin Causes relaxation of the structure. Chromatin relaxation and extension allows and facilitates the expression of genes involved in the differentiation process, such as p21 ^CIP1 . In fact, HDI, such as SAHA, sodium butyrate, has been shown to induce maturation in various human leukemia cell lines. Surprisingly, after HDAC inhibitor treatment, RAD51 expression levels are down-regulated rather than enhanced.

  Mammalian HDACs are classified into three large classes, Rpd3 (Class I), Hdal (Class II), and Sir2 / Hst (Class III), based on their structural or sequence homologues to three different yeast HDACs Is done. As Rpd3 homology class I, HDAC1, 2, 3, 8 and 11 as Hdal homology class II, HDAC4, 5, 6, 7, 9 (9a and 9b) and 10 as Sir2 / Hst homology classes III includes SIR T1, 2, 3, 4, 5, 6, and 7. Recent studies have revealed additional families of cellular factors that possess endogenous HAT or HDAC activity. These appear to be non-histone proteins that participate in the control of the cell cycle, DNA repair and transcription. A number of transcriptional activation cofactors, including but not limited to p400AF, BRCA2 and ATM-like proteins, function as HAT. Some transcriptional repressors exhibit HDAC activity by recruiting common chromatin-modified complexes in the context of chromatin. For example, the Mas protein family (Mas1, Mxi1, Mad3 and Mad4) is the basic helix-loop-helix-loop- of transcription factors that are heterodimerized by Max at their DNA binding sites. Includes helix-zipper class. Mad: Max heterodimers act as transcriptional repressors at their DNA binding sites by recruitment of “repressor complexes”. Mutations that prevent interaction with either Max or msin3 co-inhibitor complex are unable to inhibit cell growth. Thus, an HDAC inhibitor, as used herein, refers to any agent that can inhibit HDAC activity from any of the previously described proteins.

  As used herein, the terms “histone deacetylase” and “HDAC” refer to any one of a family of enzymes that remove the acetyl group from the ε-amino group of the N-terminal lysine residue of histone. Unless the text indicates otherwise, the term “histone” is meant to refer to any histone protein, including H1, H2A, H2B, H3, H4 and H5 from any species. Human HDAC proteins or gene products include HDAC-1, HDAC-2, HDAC-3, HDAC4, HDAC-5, HDAC-6, HDAC-7, HDAC-8, HDAC-9, HDAC-10 and HDAC-11 However, it is not limited to these. In some embodiments, HDAC is also derived from protozoan or fungal sources.

  Inhibitors of HDAC have been studied for their therapeutic effect on cancer cells. For example, butyric acid and its derivatives including sodium phenylbutyrate have been reported to induce apoptosis in vitro in human colon cancer, leukemia and retinoblastoma cell lines. However, butyric acid and its derivatives are not useful pharmacological agents because they tend to metabolize quickly and have a very short half-life in vivo. Other inhibitors of HDAC whose anticancer effects have been extensively studied are trichostatin A and trapoxin.

  The terms “inhibitor of histone deacetylase”, “inhibitor of histone deacetylase”, “inhibitor of HDAC” and “inhibitor of HDAC” interact with HDAC and its activity, more specifically the enzyme Used interchangeably to identify compounds that can inhibit activity. Inhibiting HDAC enzyme activity means reducing the ability of HDAC and removing acetyl groups from histones. In some embodiments, such inhibition is specific, i.e., an HDAC inhibitor reduces the ability of HDAC and produces an inhibitor of an inhibitor necessary to produce some other unrelated biological effect. The acetyl group is removed from the histone at a lower concentration.

  As HDAC inhibitors, (1) short chain fatty acids such as butyric acid ester, 4-phenyl butyrate or valproic acid, (2) hydroxamic acids such as suberoylanilide hydroxamic acid (SAHA), biaryl hydroxamate A-161906 , Bicyclic aryl-N-hydroxycarboxamide, CG-1521, PXD-101, sulfonamide hydroxamic acid, LAQ-824, oxamflatin, scriptaid, m-carboxycinnamic acid bishydroxamic acid, trapoxin-hydroxamic acid analog, Trichostatin-like trichostatin A (TSA), bishydroxamide oxamflatin m-carboxycinnamate (CBHA), ABHA, scriptaid, pyroxamide, and propenamide, (3) an epoxy ketone-containing cyclic compound Lapeptides such as trapoxin, apidicin, depsipeptide, HC-toxin, clamidosine, diheteropeptin, WF-3161, Cyl-1, and Cyl-2, (4) benzamide or non-epoxy ketone containing cyclic tetrapeptides such as FR901228, apicidin, cyclic hydroxamic acid containing peptides (CHAP), benzamides, MS-275 (MS-27-275), and CI-994, (5) depudecin, (6) PXD101, and (7) organic sulfur Compounds, but are not limited to these. Additional examples of HDAC inhibitors include TSA, TPXA and B, oxamflatin, FR901228 (FK228), trapoxin B, CHAP1, aroyl-pyrrolylhydroxyamides (APHA), apicidin, and depudecin.

  In some embodiments, the HDAC inhibitor is a reversible inhibitor and is administered before and / or during the administration of radiation and / or chemotherapy, and optionally after radiation and / or chemotherapy. Will continue. In some embodiments, the HDAC inhibitor is selected from among compounds selected from the group consisting of trichostatin A, FR, M344, SAHA, combinations thereof, and the like. Methods for determining HDAC activity in vivo or in vitro are known.

  In some embodiments, HDAC inhibitors are used in combination therapy with chemical agents that are believed to mimic the effects of radiation therapy and / or chemical agents that function by direct contact with DNA, such as DNA alkylating agents. use. In some embodiments, agents used in combination with HDAC inhibitors in the provided methods include cisplatin, adriamycin (doxorubicin), topoisomerase inhibitor (etoposide), 5-FU, and taxol.

According to this embodiment, the HDAC inhibitor is used synergistically in an effective amount that results in a concentration in the fluid of the target tissue that is less than about twice the IC ₅₀ concentration of the particular compound. In some embodiments, the effective amount is approximately equal to the IC ₅₀ concentration. In another embodiment, the HDAC inhibitor is administered at a lower concentration, such as about 50% or less of the IC ₅₀ concentration, in the target tissue. Further, in other embodiments, the HDAC inhibitor is administered locally such that the concentration at the target tissue is within the effective range, otherwise lower.

  In some other embodiments, any inhibitor of HDAC that provides a synergistic effect in combination with radiation therapy or chemotherapy is in accordance with the methods described herein, but the inhibitor has low toxicity that is acceptable to the host. Used in.

In some embodiments, the desired characteristics of an HDAC inhibitory synergist are listed below. That is, high inhibitory activity at low concentrations (eg, having an IC ₅₀ of less than about 800 ng / ml, less than about 320 ng / ml, or less than about 60 ng / ml, ie, about 5 ng / ml), reversible HDAC inhibition, synergy Low toxicity at moderate doses, quick clearance after treatment. Although acceptable combinations of these features include compromises in one or more categories, the advantages of the described methods and pharmaceutical compositions are best achieved with a combination of these features.

In some embodiments, a method provided herein comprises adding at least one compound having the structure of formula (A) or formula (I) to a cell or patient, and (1) of RAD51 Inhibitory activity, (2) disruption of RAD51 foci formation, (3) disruption of construction of functional repair complex for homologous recombination of DNA, (4) DSB repair, (5) homologous recombination, ( 6) determining sensitivity to ionizing radiation and / or (7) determining an effect in class switch recombination.
Representative compounds

Selected compounds for use in the compositions and methods described herein are shown in Tables I-IV. Formula (I) wherein R ¹ and R ³ are hydrogen, Ar ¹ is phenyl, Ar ² and Y are
Compound).

Formula (I) wherein R ¹ is hydrogen, Ar ¹ is phenyl, and R ³ , Ar ² and Y are
Compound).

A compound of formula (I) wherein R ¹ and R ³ are hydrogen, Ar ¹ is phenyl and Ar ² and Y are as defined in Table I below:
It is.

And the compound name is as follows.
N-hydroxy-4- [2- (benzothiophen-2-ylcarbonylamino) ethoxy] -benzamide, N-hydroxy-4- [2- (benzofuran-2-ylcarbonylamino) ethoxy] -benzamide, N-hydroxy -4- [2- (1H-Indol-2-ylcarbonylamino) ethoxy] -benzamide, N-hydroxy-4- [2- (1-methylindol-2-ylcarbonylamino) ethoxy] -benzamide, N- Hydroxy-4- [3- (benzothiophen-2-ylcarbonylamino) propoxy] -benzamide, N-hydroxy-4- [3- (benzofuran-2-ylcarbonylamino) propoxy] -benzamide, N-hydroxy-4 -[2S- (benzothiophen-2-ylcarbonylamino) -3 Methylbutoxy] -benzamide, N-hydroxy-4- [2S- (benzothiophen-2-ylcarbonylamino) butoxy] -benzamide, N-hydroxy-4- [2S- (benzothiophen-2-ylcarbonylamino)- Propoxy] -benzamide, N-hydroxy-4- [2R- (benzothiophen-2-ylcarbonylamino) -propoxy] -benzamide, N-hydroxy-4- [2S- (benzofuran-2-ylcarbonylamino) butoxy] -Benzamide, N-hydroxy-4- [2- (benzothiophen-2-ylcarbonylamino) -1R-methylethoxy] -benzamide, N-hydroxy-4- [2- (benzothiophen-2-ylcarbonylamino) -1S-methylethoxy] -benzamide, N- Droxy-4- [2- (benzofuran-2-ylcarbonylamino) -1R-methylethoxy] -benzamide, N-hydroxy-4- [2- (6-methoxybenzothiophen-2-ylcarbonylamino) ethoxy]- Benzamide, N-hydroxy-4- [2- (5-methylbenzothiophen-2-ylcarbonylamino) ethoxy] -benzamide, N-hydroxy-4- [2- (3-chlorobenzothiophen-2-ylcarbonylamino) ) Ethoxy] -benzamide, N-hydroxy-4- [2- (5-methylbenzofuran-2-ylcarbonylamino) ethoxy] -benzamide, N-hydroxy-4- [2- (6-methylbenzofuran-2-yl) Carbonylamino) ethoxy] -benzamide, N-hydroxy-4- [2- (4 -Trifluoromethylbenzothiophen-2-ylcarbonylamino) ethoxy] -benzamide, N-hydroxy-4- [2- (5-fluorobenzothiophen-2-ylcarbonylamino) ethoxy] -benzamide, N-hydroxy-4 -[2- (5-methoxybenzofuran-2-ylcarbonylamino) ethoxy] -benzamide, N-hydroxy-4- [2- (5-chlorobenzofuran-2-ylcarbonylamino) ethoxy] -benzamide, N-hydroxy -4- [2- (7-methoxybenzofuran-2-ylcarbonylamino) ethoxy] -benzamide, N-hydroxy-4- [2- (5-methoxybenzofuran-2-ylcarbonylamino) ethoxy] -benzamide, N -Hydroxy-4- {2- [5- (2-methoxy) Ethoxy) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- {2- [5- (2-morpholin-4-ylethoxy) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N -Hydroxy-4- {2- [5- (pyridin-3-ylmethoxy) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- [2- (3-methylbenzofuran-2-ylcarbonyl) Amino) ethoxy] -benzamide, N-hydroxy-4- [2- (3-methylbenzothiophen-2-ylcarbonylamino) ethoxy] -benzamide, N-hydroxy-4- {2- [5- (2-hydroxy Ethoxy) benzofuran-2-ylcarbonylamino] ethoxy} benz N-hydroxy-4- {2- [5- (2-N, N-dimethylaminoethoxy) benzofuran-2-ylcarbonylamino] -ethoxy} -benzamide, N-hydroxy-4- {2- [6 -(2-methoxyethoxy) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- {2- [6- (2-morpholin-4-ylethoxy) benzofuran-2-ylcarbonylamino] ethoxy } -Benzamide, N-hydroxy-4- {2- [6- (pyridin-3-ylmethoxy) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- [2- (3-ethylbenzofuran) -2-ylcarbonylamino) ethoxy] -benzamide, N-hydroxy-4- [2- (5-phenyl) Luoloindol-2-ylcarbonylamino) ethoxy] -benzamide, N-hydroxy-4- [2- (5-methoxyindol-2-ylcarbonylamino) ethoxy] -benzamide, N-hydroxy-4- {2- [3- (Methoxymethyl) benzofuran-2-ylcarbonylamino] ethoxy} benzamide, N-hydroxy-4- {2- [3- (phenoxymethyl) benzofuran-2-ylcarbonylamino] ethoxy} benzamide, N-hydroxy -4- [2- (5,6-dimethoxyindol-2-ylcarbonylamino) ethoxy] -benzamide, N-hydroxy-4- {2- [3- (morpholin-4-ylmethyl) benzolfuran-2-yl Carbonylamino] ethoxy} -benzamide, N-hydroxy-4- { -[3- (N, N-dimethylaminomethyl) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- {2- [3- (i-propoxymethyl) benzofuran-2-ylcarbonyl Amino] ethoxy} benzamide, N-hydroxy-4- {2- [7- (phenoxymethyl) benzofuran-2-ylcarbonylamino] ethoxy} benzamide, N-hydroxy-4- {2- [7- (methoxymethyl) Benzofuran-2-ylcarbonylamino] ethoxy} benzamide, N-hydroxy-4- {2- [7- (morpholin-4-ylmethyl) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- {2- [7- (N, N-dimethylaminomethyl) benzofuran-2 Ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- {3- (5- (methyl) benzothiophen-2-ylcarbonylamino] propoxy} -benzamide, N-hydroxy-4- {3- [6- (Methoxy) benzothiophen-2-ylcarbonylamino] propoxy} -benzamide, N-hydroxy-4- {3- [7- (methoxymethyl) benzofuran-2-ylcarbonylamino] propoxy} -benzamide, N-hydroxy- 4- {3- [7- (phenoxymethyl) benzofuran-2-ylcarbonylamino] propoxy} -benzamide, N-hydroxy-4- {2- [5- (2-methoxyethoxy) benzofuran-2-ylcarbonylamino ] -1R-methylethoxy} benzamide, N-hydroxy- 4- (2R-benzofuran-2-ylcarbonylamino-3-methylthiopropoxy) benzamide, N-hydroxy-4- (2R-benzofuran-2-ylcarbonylamino-3-methylsulfonylpropoxy) benzamide, N-hydroxy-4 -{2- [3- (2-phenylethyl) benzofuran-2-ylcarbonylamino] ethoxy} benzamide, N-hydroxy-4- {2- [3- (N-methyl-N-benzylaminomethyl) benzofuran- 2-ylcarbonylamino] -ethoxy} benzamide, N-hydroxy-4- {2- [3- (N-methyl-N-2-phenylethylaminomethyl) benzofuran-2-ylcarbonylamino] -ethoxy} benzamide, N-hydroxy-4- {2- [3- (3-hydroxypropyl Omethyl) benzofuran-2-ylcarbonylamino] -ethoxy} benzamide, N-hydroxy-4- {2- [3- (3-hydroxypropylsulfinylmethyl) benzofuran-2-ylcarbonylamino] -ethoxy} benzamide, N- Hydroxy-4- {2- [3- (3-hydroxypropylsulfonylmethyl) benzofuran-2-ylcarbonylamino] -ethoxy} benzamide, N-hydroxy-4- {2- [3- (N-methyl-N- 2-Indol-3-ylethylaminomethyl) benzofuran-2-ylcarbonylamino] -ethoxy} benzamide, N-hydroxy-4- {2- [3- (2- (3- (trifluoromethylphenyl) ethyl) benzofuran -2-ylcarbonylamino] -ethoxy} benzamide, -Hydroxy-4- {2- [3- {2- (3-trifluoromethoxyphenyl) ethyl) benzofuran-2-ylcarbonylamino] -ethoxy} benzamide, N-hydroxy-4- {2- [3- ( N-hydroxyaminocarbonylmethylaminomethyl) benzofuran-2-ylcarbonylamino] ethoxy} benzamide, N-hydroxy-4- {2- [3- (2-carboxyethylaminomethyl) benzofuran-2-ylcarbonylamino]- Ethoxy} benzamide, N-hydroxy-4- [2- (benzofuran-2-ylcarbonylamino) -1RS-phenoxymethylethoxy} -benzamide, N-hydroxy-4- {2- [3- (3-hydroxypropoxymethyl) ) Benzofuran-2-ylcarbonylamino] ethoxy}- Benzamide, N-hydroxy-4- {2- [3- (2-fluorophenoxymethyl) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- {2- [3- (3-fluoro Phenoxymethyl) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- {2- [3- (4-fluorophenoxymethyl) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N- Hydroxy-4- {2- [3- {2-methoxyethyloxymethyl) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- {2- [3- (pyridin-4-yloxy) Methyl) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide N-hydroxy-4- {2- [3- (2,4,6-trifluorophenoxymethyl) benzofuran-2-ylcarbonylamino] -ethoxy} benzamide, N-hydroxy-4- {2- [3- ( 2-oxopyridin-1-ylmethyl) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- {2- [3- (2,2,2-trifluoroethoxymethyl) benzofuran-2- Ylcarbonylamino] -ethoxy} benzamide, N-hydroxy-4- {2- [3- (4-imidazol-1-ylphenoxymethyl) benzofuran-2-ylcarbonylamino] -ethoxy} benzamide, N-hydroxy-4 -{2- [3- (4- [1.2.4] -Triazin-1-ylphenoxymethyl) benzofura -2-ylcarbonylamino] ethoxy} benzamide, N-hydroxy-4- {2- [3- (pyrrolidin-1-methyl) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- { 2- [3- (Piperidin-1-methyl) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- {2- [3- (4-trifluoromethylpiperidine-1-methyl) benzofuran -2-ylcarbonylamino] -ethoxy} benzamide, N-hydroxy-4- {2- [3- (4-methylpiperazin-1-methyl) benzofuran-2-ylcarbonylamino] -ethoxy} benzamide, N-hydroxy -4- {2- [3- (3,3,3-trifluoropropyloxymethyl) benzo Furan-2-ylcarbonylamino] -ethoxy} benzamide, N-hydroxy-4- [2- (4-methylbenzofuran-2-ylcarbonylamino) ethoxy] benzamide, N-hydroxy-4- {2- [3- (4-Fluorophenylthiomethyl) benzofuran



-2-ylcarbonylamino] -ethoxy} -benzamide, N-hydroxy-4- {2- [3- (4-fluorophenylsulfinylmethyl) benzofuran-2-ylcarbonylamino] -ethoxy} benzamide, N-hydroxy- 4- {2- [3- {4-Fluorophenylsulfonylmethyl) benzofuran-2-ylcarbonylamino] -ethoxy} benzamide, N-hydroxy-4- {2S- [3- (2,2,2-trifluoro) Ethoxymethyl) benzofuran-2-ylcarbonylamino] -butoxy) benzamide, N-hydroxy-4- [2- (4-hydroxybenzofuran-2-ylcarbonylamino) ethoxy] benzamide, N-hydroxy-4- [2S- (5-Chlorobenzofuran-2-ylcarbonylamino) but Ci] benzamide, N-hydroxy-4- [2- (5-chlorobenzofuran-2-ylcarbonylamino] -1R-methylethoxy] benzamide, N-hydroxy-4- [2- (4-pyridin-3-yl) Methyloxymethylbenzofuran-2-ylcarbonylamino) ethoxy] benzamide, N-hydroxy-4- [2- (4-methoxybenzofuran-2-ylcarbonylamino) ethoxy] benzamide, N-hydroxy-4- {2- [ 4- (2-methoxyethyloxy) benzofuran-2-ylcarbonylamino) ethoxy} -benzamide, N-hydroxy-4- [2- (4-pyridin-3-ylmethyloxybenzofuran-2-ylcarbonylamino) ethoxy Benzamide, N-hydroxy-4- [2- (4-methoxyi) Dole-2-ylcarbonylamino) ethoxy] benzamide, N-hydroxy-4- {2S- [3- (2-methoxyethyloxymethyl) benzofuran-2-ylcarbonylamino] -butoxy} benzamide, N-hydroxy-4 -{2- [3- (2-methoxyethyloxymethyl) benzofuran-2-ylcarbonylamino] -1R-methylethoxy} benzamide, N-hydroxy-4- {2- [3- (N, N-diethylaminomethyl) ) Benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- {2S- [5- (2-methoxyethyloxy) benzofuran-2-ylcarbonylamino] butoxy} -benzamide, N-hydroxy- 4- {2- [5- (tetrahydropyran-4-yloxy) be Nzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- {2S- [5- (tetrahydropyran-4-yloxy) benzofuran-2-ylcarbonylamino] butoxy} -benzamide, N-hydroxy- 4- {2- [5- (tetrahydropyran-4-yloxy) benzofuran-2-ylcarbonylamino] -lR-methyl-ethoxy} benzamide, N-hydroxy-4- {2- [5- (2,2, 2-trifluoroethyloxy) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- {2- [5- (2-pyrrolidin-1-ylethyloxy) benzofuran-2-ylcarbonylamino ] Ethoxy} -benzamide, N-hydroxy-4- {2S- [5- (2 Pyrrolidin-1-ylethyloxy) benzofuran-2-ylcarbonylamino] butoxy} -benzamide, N-hydroxy-4- {2- [5- (2-pyrrolidin-1-ylethyloxy) benzofuran-2-ylcarbonyl Amino] -lR-methylethoxy} benzamide, N-hydroxy-4- {2- [5- (piperidin-4-yloxy) benzofuran-2-ylcarbonylamino] ethoxy} -benzamide, N-hydroxy-4- [2S -(Benzofuran-2-ylcarbonylamino) -4-methylthiobutoxy] benzamide and N-hydroxy-4- [2S- (benzofuran-2-ylcarbonylamino) -4-methylsulfonylbutoxy] benzamide.

Formula (I) wherein R ¹ and R ³ are hydrogen, Ar ¹ is isoxazol-5-yl, and Ar ² and Y are
Compound).
Specific embodiments

  Specific embodiments are described below.

I. Compounds of formula (I) in group I are
(Where
R ¹ is hydrogen or alkyl;
X is —O—, —NR ² — or —S (O) _n , wherein n is 0-2 and R ² is hydrogen or alkyl;
Y is alkylene optionally substituted with cycloalkyl, optionally substituted phenyl, alkylthio, alkylsulfonyl, optionally substituted phenylalkylthio, optionally substituted phenylalkylsulfonyl or hydroxy;
Ar ¹ is phenylene or heteroarylene, wherein said Ar ¹ is optionally substituted with one or two groups independently selected from alkyl, halo, hydroxy, alkoxy, haloalkoxy or haloalkyl And
R ³ is hydrogen, alkyl, hydroxyalkyl, or optionally substituted phenyl;
Ar ² is aryl, aralkyl, aralkenyl, heteroaryl, heteroaralkyl, heteroaralkenyl, cycloalkyl, cycloalkylalkyl, heterocycloalkyl, or heterocycloalkylalkyl. )
It is.

  In this group I,

(A) One compound group is a compound group in which R ¹ and R ³ are hydrogen, X is —O—, and Y is ethylene or n-propylene. In one embodiment, Y is ethylene.

(B) In another compound group, R ¹ and R ³ are hydrogen, X is —O—, and Y is —CH (C ₂ H ₅ ) CH ₂ —, —CH (J—C ₃ H ₇ ) CH ₂ —, or —CH (CH ₃ ) CH ₂ —, and the chiral carbon stereochemistry is (S). In one embodiment, Y is —CH (C ₂ H ₅ ) CH ₂ —.

(C) Yet another group of compounds is: wherein R ¹ and R ³ are hydrogen, X is —O—, Y is —CH ₂ CH (CH ₃ ) —, and a chiral carbon stereo The chemistry is the group of compounds that are (R).

(I) Within groups (A)-(C), one group of compounds is: wherein Ar ¹ is phenylene, wherein the hydroxamate and the X group are para to each other and Ar ² is a group of compounds that are aryl. In some embodiments, Ar ² is phenyl, optionally methoxy, ethoxy, phenyl, methyl, tert-butyl, pyrrol-1-yl, cyclohexen-3-oxy, pyridin-3-yl, pyridine-2 -Substituted with one or two substituents independently selected from yl, benzoylamino, fluoro, chloro or thiophen-2-ylmethoxy. In some embodiments, Ar ² is phenyl, 4-biphenyl, 3-biphenyl, 4-tert-butylphenyl, 4-pyrrol-1-ylphenyl, 4- (cyclohexen-3-oxy) phenyl, 4- (Pyridin-2-yl) phenyl, 4- (pyridin-3-yl) -phenyl, 2,4-difluorophenyl, 3,4-dimethoxyphenyl, 3,5-dimethoxyphenyl, 3,4-difluorophenyl, 2 , 5-dimethylphenyl, 2,3-dichlorophenyl, 2,3-dimethylphenyl, 4-chloro-2-methoxyphenyl, 3-ethoxyphenyl, 4-methoxy-2-methylphenyl, 3-fluoro-4-methoxyphenyl 2-thiophen-2-ylmethoxyphenyl, 3-thiophen-2-ylmethoxyphenyl, 2-bif Cycloalkenyl, or 2-pyrrol-1-yl-phenyl.

(Ii) Within groups (A)-(C), another group of compounds is: wherein Ar ¹ is phenylene, wherein the hydroxamate and X groups are para to each other and Ar ² Is a group of compounds where trans-aryl-CH = CH-. In some embodiments, Ar ² is trans-phenyl-CH═CH—, optionally substituted with alkoxy. In one embodiment, Ar ² is trans-phenyl-CH═CH— substituted with methoxy. In one embodiment, Ar ² is trans-phenyl-CH═CH—.

(Iii) Within groups (A)-(C), another group of compounds is: wherein Ar ¹ is phenylene, wherein the hydroxamate and X groups are para to each other and Ar ² Is heteroaryl-CH = CH-. In one embodiment, Ar ² is pyridinyl -CH = CH-. In one embodiment, Ar ² is, trans-5-bromo-thiophen-2-yl -CH = CH-, or trans- indol-3-yl -CH = a CH-.

(Iv) Within groups (A)-(C), another group of compounds is: wherein Ar ¹ is phenylene, wherein the hydroxamate and the X group are para to each other and Ar ² Is a group of compounds that are heteroaryl. In some embodiments, Ar ² is pyridin-3-yl, thiophen-2-yl, quinolin-6-yl, thiazol-2-yl, benzthiazol-2-yl, benzoxazol-2-yl, furanyl, Pyrrol-2-yl, indol-5-yl, indol-3-yl, indazol-3-yl, quinolin-3-yl, quinolin-1-yl, quinolin-8-yl, benzotriazol-4-yl, benzofuran -5-yl, isoquinolin-1-yl, isoquinolin-3-yl, quinoxalin-2-yl, quinolin-2-yl, or benzimidazol-5-yl, wherein the ring is optionally phenyl, pyridine-4-yl Substituted with yl, methyl, methoxy or dimethylaminomethyl.

(V) Within groups (A)-(C), another group of compounds is: wherein Ar ¹ is phenylene, wherein the hydroxamate and the X group are para to each other and Ar ² Is indol-2-yl, benzofuran-2-yl or benzothiophen-2-yl, which are optionally alkyl, alkoxy, halo, haloalkyl, alkoxyalkyloxy, optionally substituted heterocycloalkylalkyl Substituted with oxy, optionally substituted heteroaralkyloxy, hydroxyalkoxy, aminoalkyl, aminoalkyloxy, alkoxyalkyloxy, alkoxyalkyl, optionally substituted phenyloxyalkyl, or optionally substituted heterocycloalkylalkyl It is a compound group. In some embodiments, Ar ² is benzofuran-2-yl or benzothiophen-2-yl, wherein benzofuran-2-yl or benzothiophen-2-yl is optionally methoxy, methyl, Chloro, trifluoromethyl, fluoro, 2-methoxyethoxy, 2-morpholin-4-ylethoxy, pyridin-3-ylmethoxy, 2-hydroxyethoxy, 2-N, N-dimethylaminoethoxy, ethyl, methoxymethyl, 2-propyl Substituted with oxymethyl, phenoxymethyl, morpholin-4-ylmethyl or N, N-dimethylaminomethyl located in the 3- or 5-position. In one embodiment, Ar ² is optionally substituted at the 3-position between benzothiophen-2-yl or benzofuran-2-yl. In one embodiment, Ar ² is benzofuran-2-yl, 3-N, N-dimethylaminomethylbenzofuran-2-yl, or 3-phenoxymethylbenzofuran-2-yl.

(Vi) Within groups (A)-(C), another group of compounds is: wherein Ar ¹ is phenylene, wherein the hydroxamate and the X group are para to each other and Ar ² is indol-2-yl, benzofuran-2-yl or benzothiophen-2-yl and is substituted with phenyloxyalkyl, substituted heteroaryloxyalkyl, substituted heterocycloalkyloxyalkyl, or haloalkoxyalkyl These are a group of compounds located at the 3-position of the benzothiophen-2-yl and benzofuran-2-yl rings. In one embodiment, Ar ² is 3- (2,2,2-trifluoroethyloxymethyl) benzofuran-2-yl.

(Vii) Within groups (A)-(C), another group of compounds is a group of compounds wherein Ar ¹ is heteroarylene and Ar ² is aryl. In some embodiments, Ar ¹ is a 5-membered heteroarylene ring comprising 1, 2 or 3 heteroatoms independently selected from N, O or S. In some embodiments, Ar ¹ is isoxazolyl, wherein the hydroxamate and X groups are located at the 5- and 3-positions of the isoxazolyl ring, and the oxygen atom in the ring is at the 1-position. And Ar ² is aryl. In some embodiments, Ar ² is phenyl optionally substituted with one or two substituents independently selected from methoxy, ethoxy, and optionally ethoxy or methyl, methyl, tert- Phenyl substituted with butyl, pyrrol-1-yl, cyclohexen-3-oxy, pyridin-3-yl, pyridin-2-yl, benzoylamino, fluoro, chloro or thiophen-2-ylmethoxy. In some embodiments, Ar ² is phenyl, 4-biphenyl, 3-biphenyl, 2- (2-ethoxyphenyl) phenyl, 3-methylbiphen-4-yl, 4-tert-butylphenyl, 4-pyrrole- 1-ylphenyl, 4- (cyclohexen-3-oxy) phenyl, 4- (pyridin-2-yl) phenyl, 4- (pyridin-3-yl) -phenyl, 2,4-difluorophenyl, 3,4- Dimethoxyphenyl, 3,5-dimethoxyphenyl, 3,4-difluorophenyl, 2,5-dimethylphenyl, 2,3-dichlorophenyl, 2,3-dimethylphenyl, 4-chloro-2-methoxyphenyl, 3-ethoxyphenyl 4-methoxy-2-methylphenyl, 3-fluoro-4-methoxyphenyl, 2-thiophen-2-ylme Toxiphenyl, 3-thiophen-2-ylmethoxyphenyl, 2-biphenyl, or 2-pyrrol-1-ylphenyl.

(Viii) Within groups (A)-(C), another group of compounds is a group of compounds wherein Ar ¹ is heteroarylene and Ar ² is aryl-CH═CH—. In some embodiments, Ar ¹ is a 5-membered heteroarylene ring comprising 1, 2 or 3 heteroatoms independently selected from N, O or S. In some embodiments, Ar ¹ is isoxazolyl, wherein the hydroxamate and X groups are located at the 5- and 3-positions of the isoxazolyl ring and the oxygen atom in the ring is at the 1-position. Yes, Ar ² is phenyl-CH═CH—, optionally substituted with alkoxy.

(Ix) Within groups (A) to (C), another group of compounds is a group of compounds wherein Ar ¹ is heteroarylene and Ar ² is heteroaryl-CH═CH—. In some embodiments, Ar ¹ is a 5-membered heteroarylene ring comprising 1, 2 or 3 heteroatoms independently selected from N, O or S. In some embodiments, Ar ¹ is isoxazolyl, wherein the hydroxamate and X groups are located at the 5- and 3-positions of the isoxazolyl ring and the oxygen atom in the ring is at the 1-position , Ar ² is pyridinyl -CH = CH-.

(X) Within groups (A)-(C), another group of compounds is a group of compounds wherein Ar ¹ is heteroarylene and Ar ² is heteroaryl. In some embodiments, Ar ¹ is a 5-membered heteroarylene ring comprising 1, 2 or 3 heteroatoms independently selected from N, O or S. In some embodiments, Ar ¹ is isoxazolyl, wherein the hydroxamate and X groups are located at the 5- and 3-positions of the isoxazolyl ring, and the oxygen atom in the ring is at the 1-position. And Ar ² is pyridin-3-yl, thiophen-2-yl, quinolin-6-yl, thiazol-2-yl, benzthiazol-2-yl, benzoxazol-2-yl, furanyl, pyrrol-2-yl Yl, indol-5-yl, indol-3-yl, indazol-3-yl, quinolin-3-yl, quinolin-8-yl, benzotriazol-4-yl, isoquinolin-1-yl, isoquinolin-3-yl, quinoxaline -2-yl, quinolin-2-yl, or benzimidazol-5-yl, wherein the ring is optionally phenyl, pyridine-4- Rumechiru is substituted with methoxy or dimethylaminomethyl.

(Xi) Within groups (A)-(C), another group of compounds is: wherein Ar ¹ is heteroarylene and Ar ² is indol-2-yl, benzofuran-2-yl, or benzothiophene 2-yl, which is optionally alkyl, alkoxy, halo, haloalkyl, alkoxyalkyloxy, optionally substituted heterocycloalkylalkyloxy, optionally substituted heteroaralkyloxy, hydroxyalkoxy, aminoalkyl A group of compounds substituted with oxy, alkoxyalkyloxy, alkoxyalkyl, optionally substituted phenyloxyalkyl, or optionally substituted heterocycloalkylalkyl. In some embodiments, Ar ¹ is a 5-membered heteroarylene ring comprising 1, 2 or 3 heteroatoms independently selected from N, O or S. In some embodiments, Ar ¹ is isoxazolyl, wherein the hydroxamate and X groups are located at the 5- and 3-positions of the isoxazolyl ring and the oxygen atom in the ring is at the 1-position , Ar ² are benzofuran-2-yl and benzothiophen-2-yl, which are optionally methoxy, methyl, chloro, trifluoromethyl, fluoro, 2-methoxyethoxy, 2-morpholin-4-ylethoxy , Pyridin-3-ylmethoxy, 2-hydroxyethoxy, 2-N, N-dimethylaminoethoxy, ethyl, methoxymethyl, phenoxymethyl, morpholin-4-ylmethyl or dimethylaminomethyl and benzothiophen-2-yl And at the 3-position of the benzofuran-2-yl ring. In one embodiment, Ar ² is benzofuran-2-yl or 3-phenoxymethylbenzofuran-2-yl.

(Xii) Within groups (A) and (B), another group of compounds is: wherein Ar ² is alkoxyalkyloxy, optionally substituted heterocycloalkylalkyloxy, hydroxyalkoxy, aminoalkyloxy, alkoxy A group of compounds substituted with alkyloxy, alkoxyalkyl, optionally substituted phenyloxyalkyl, optionally substituted heteroaryloxyalkyl, or optionally substituted heterocycloalkylalkyl. Within this group, one compound group is a group of compounds where Ar ¹ and Ar ² are as described in the previous embodiment.

II. Group II of compounds of formula (I) is a group of compounds wherein X is —O— and R ¹ and R ³ are hydrogen.

III. Group III of compounds of formula (I) is a group of compounds wherein X is —S (O) _n and R ¹ and R ³ are hydrogen.

  Within the above Groups II and III, in some embodiments, Y is alkylene.

  Within the above groups II and III, in some embodiments, Y is cycloalkyl, optionally substituted phenyl, alkylthio, alkylsulfinyl, alkylsulfonyl, optionally substituted phenylalkylthio, optionally substituted phenyl. Alkylsulfonyl, hydroxyl, or alkylene substituted with optionally substituted phenoxy.

Within groups II and III above, in some embodiments, Ar ¹ is phenylene.

Within groups II and III above, in some embodiments, Ar ¹ is heteroarylene.

Within groups II and III above, in some embodiments, Ar ¹ is phenylene. In some embodiments, the —CONHOH and X groups are at the 1- or 4-position of the phenylene ring.

IV. Group IV of the compound of formula (I) is a group wherein Ar ¹ is phenylene, X is —O—, R ¹ and R ³ are hydrogen, —CONHOH and the X group are 1- Or a group of compounds in the 4-position.

  Within the above group IV, in some embodiments, Y is alkylene.

  Within the above group IV, in some embodiments, Y is cycloalkyl, optionally substituted phenyl, alkylthio, alkylsulfinyl, alkylsulfonyl, optionally substituted phenylalkylthio, optionally substituted phenylalkylsulfonyl. , Hydroxyl, or optionally substituted alkylene substituted with phenoxy.

(I) Among the above groups II, III and IV, and the specific groups described therein, in some embodiments, Ar ² is aryl (C _2-3 ) alkenyl. In some embodiments, Ar ² has the formula:

Wherein phenyl is optionally substituted with 1 or 2 substituents independently selected from alkyl, alkoxymethylenedioxy, dialkylamino or hydroxy)
It is represented by In some embodiments, the substituent is selected from the group consisting of alkyl, alkoxy, methylenedioxy, or hydroxy.

In some embodiments, Ar ² is trans-phenyl-CH═CH—, trans-4-MeO-phenyl-CH═CH—, trans-3,4-methylenedioxyphenyl CH═CH—, trans— 3-hydroxyphenyl-CH = CH-, trans-4-hydroxyphenyl-CH = CH-, trans-2-methoxyphenyl-CH = CH-, trans-3-methoxyphenyl-CH = CH-, trans-3- Tolyl-CH = CH-, trans-4-tolyl-CH = CH-, trans-4-dimethylaminophenyl-CH = CH-, tarance 2-tolyl-CH = CH-, or trans-2-hydroxyphenyl-CH = CH-.

(Ii) Among the above groups II, III and IV, and the groups described therein, in some embodiments, Ar ² is heteroaryl (C _2-3 ) alkenyl. In some embodiments, Ar ² is trans-heteroaryl-CH═CH—, or trans-heteroaryl-C (CH ₃ ) ═CH—. In some embodiments, the heteroaryl ring of Ar ² is pyridinyl optionally substituted with 1 or 2 substituents selected from hydroxyl, alkoxy, halo, or optionally substituted heterocycloalkoxy. , Benzofuranyl, thienyl (thiophene), furanyl, or indolyl.

In some embodiments, Ar ² is trans-pyridin-3-yl-CH═CH—, trans-5-hydroxybenzofuran-2-yl-C (CH ₃ ) ═CH—, trans-5- (1 - cyclopropyl piperidin-4-yloxy) benzofuran-2-yl _{-C (CH 3) = CH-,} trans-5- methoxy-2-yl _{-C (CH 3) = CH-,} trans- benzofuran-2 Yl-CH = CH-, trans-5-bromothiophen-2-yl-CH = CH-, trans-furan-3-yl-CH = CH-, trans-thiophen-3-yl-CH = CH-, trans- thiophen-2-yl -CH = CH-, trans- benzofuran-2-yl _{-C (CH 3) = CH-,} cis- benzofuran-2 Yl _{-C (CH 3) = CH-,} trans- indol-3-yl CH = CH-, trans-7- methoxy-2-yl -CH = CH-, trans-5- methoxy-2-yl - C _(CH 3) = CH-, or trans- furan-2-yl -CH = CH.

(Iii) Among the groups II, III, and IV, and groups described therein, in some embodiments, Ar ² is aryl. In some embodiments, aryl ring substituents are optionally substituted phenyl, alkyl, alkoxy, halo, optionally substituted heteroaryl, optionally substituted cycloalkenyloxy, optionally substituted heteroaryl. Independently selected from aralkyloxy, optionally substituted heterocycloalkyl, optionally substituted phenylcarbonylamino, or methylenedioxy. In some embodiments, Ar ² is phenyl, 4-biphenyl, 3-biphenyl, 4-tert-butylphenyl, 4-pyrrol-1-ylphenyl, 4- (pyridin-3-yl) phenyl, 4- (Pyridin-2-yl) phenyl, 4- (benzoylamino) phenyl, 2,4-difluorophenyl, 3,4-methylenedioxyphenyl, 3,4-dimethoxyphenyl, 3,5-dimethoxyphenyl, 3,4 -Difluorophenyl, 2,5-dimethylphenyl, 2,3-dichlorophenyl, 2,3-dimethylphenyl, 4-chloro-2-methoxyphenyl, 3-ethoxyphenyl, 4-methoxy-2-methylphenyl, 3-fluoro -4-methoxyphenyl, 2- (thiophen-2-ylmethoxy) phenyl, 3- (thiophen-2-yl) Methoxy) -phenyl, 2-biphenyl, naphth-1-yl, 2-pyrrol-1-yl-phenyl, 4-fluoronaphth-1-yl, 3-MeO-naphth-2-yl, 2-MeO-naphtho 1-yl, naphth-2-yl, 4- (2-pyridin-4-ylthiazol-5-yl) phenyl, 4- [2- (4-methylpiperazin-1-yl) thiazol-5-yl]- Phenyl, 4- {2-pyridin-4-ylaminothiazol-5-yl) phenyl, 4- (4-methylpiperazin-1-yl) phenyl, 4- (4-hydroxypiperidin-1-yl) phenyl, 4 -(4-morpholin-4-ylmethylthiazol-2-yl) phenyl, 4- [2- (4-methylpiperazin-1-ylmethyl) thiazol-5-yl] phenyl, l-methoxyna To-2-yl, 3 ′-(2-hydroxyethyl) biphen-4-yl, 3 ′-(2-hydroxyethyl) biphen-3-yl, 2 ′-(2-hydroxyethyl) biphen-4-yl 2 ′-(2-hydroxyethyl) biphen-3-yl or 4- [4- (2-morpholin-4-ylethyl) thiazol-2-yl] phenyl.

(Iv) Among the groups II, III, and IV, and groups described therein, in some embodiments, Ar ² is heteroaryl. In some embodiments, Ar ² is heteroaryl, optionally alkyl, halo, haloalkyl, alkoxy, alkoxyalkyl, hydroxyalkoxy, hydroxyalkoxyalkyl, alkoxyalkyloxy, alkoxyalkyloxyalkyl, aminoalkyl, Aminoalkoxy, haloalkoxy, haloalkoxyalkyl, optionally substituted phenylalkyl, optionally substituted phenyloxyalkyl, optionally substituted heteroaryl, optionally substituted heteroaralkyloxy, optionally substituted hetero Aryloxyalkyl, optionally substituted heterocycloalkylalkyl, optionally substituted heterocycloalkyloxy, optionally substituted heterocycloalkylalkyloxy, -alkylene-S ( O) _n R ^a (wherein n is 0-2 and R ^a is hydroxyalkyl or optionally substituted phenyl), -alkylene-NR ^e -alkylene CONR ^c R ^d (where R is ^c is hydroxyl and R ^d and R ^e are independently hydrogen or alkyl) or substituted with 1 or 2 substituents independently selected from carboxyalkylaminoalkyl.

In some embodiments, Ar ² is thiophen-2-yl, pyridin-3-yl, quinolin-6-yl, benzothiazol-2-yl, benzoxazol-2-yl, benzofuran-2-yl, benzofuran- 5-yl, benzothien-2-yl, furan-2-yl, 1H-benzimidazol-2-yl, 1H-pyrrol-2-yl, thiazol-2-yl, 1H-indol-2-yl, 1H-indole -5-yl, 1H-indol-3-yl, quinolin-3-yl, quinolin-8-yl, 1H-indazol-3-yl, 1H-benzotriazol-5-yl, isoquinolin-1-yl, isoquinoline 3 -Yl, quinoxalin-2-yl, quinolin-2-yl, 1H-benzimidazol-5-yl, quinolin-1-yl, pyridi N-2-yl, pyridin-2-yl, quinolin-2-yl, furan-3-yl, thiophen-2-yl, or thiophen-3-yl. In some embodiments, Ar ² is benzofuran-2-yl or benzothien-2-yl, which are optionally substituted with one or two substituents as described in the previous paragraph. ing.

In some embodiments, Ar ² is benzofuran-2-yl and is monosubstituted at the 3-position, 4-position or 5-position, or disubstituted at the 4-position and 7-position. In some embodiments, the benzofuran-2-yl at Ar ² is monosubstituted at the 3- or 5-position with a substituent described in the immediately preceding paragraph. In some embodiments, the substituent is chloro, fluoro, trifluoromethyl, methyl, ethyl, methoxy, 1-cyclopropylpiperidin-4-yloxy, 1- (2,2,2-trifluoroethyl) piperidine- 4-yloxy, N, N-dimethylaminomethyl, N, N-diethylaminomethyl, 2-methoxyethoxymethyl, phenoxymethyl, 2-methoxyethoxy, 2-morpholin-4-ylethoxy, pyridin-3-ylmethoxy, 2-hydroxy Ethoxy, 2-N, N-dimethylaminoethoxy, methoxymethyl, 3-i-propoxymethyl, morpholin-4-ylmethyl, 3-hydroxypropyloxymethyl, 2-fluorophenoxymethyl, 3-fluorophenoxymethyl, 4-fluoro Phenoxymethyl, 3-methoxy Propyloxymethyl, pyridin-4-yloxymethyl, 2,4,6-trifluorophenoxymethyl, 2-oxopyridin-1-ylmethyl, 2,2,2-trifluoroethoxymethyl, 4-imidazol-1-yl Phenoxymethyl, 4- [l. 2.4-triazin-1-ylphenoxymethyl, 2-phenylethyl, pyrrolidin-1-ylmethyl, piperidin-1-ylmethyl, 4-trifluoromethylpiperidin-1-ylmethyl, 4-methylpiperazin-1-ylmethyl, 3 , 3,3-trifluoropropyloxymethyl, 4-fluorophenylthiomethyl, 4-fluorophenylsulfinylmethyl, 4-fluorophenylsulfonylmethyl, pyridin-3-ylmethyloxymethyl, tetrahydropyran-4-yloxy, 2, 2,2-trifluoroethyloxy, 2-pyrrolidin-1-ylethyloxy, piperidin-4-yloxy, N-methyl-N-benzylaminomethyl, N-methyl-N-2-phenylethylaminomethyl, 3- Hydroxypropylthiomethyl, 3 Hydroxypropylsulfinylmethyl, 3-hydroxypropylsulfonyl-methyl, N-methyl-N-2-indol-3-ylethylaminomethyl, 2- (4-trifluoromethylphenyl) ethyl, 2- (3-trifluoromethoxy Independently selected from phenyl) ethyl, N-hydroxyaminocarbonyl-methylaminomethyl, or 3- (2-carboxyethylaminomethyl).

In some embodiments, Ar ² is benzofuran-2-yl and the 3-position is N, N-dimethylaminomethyl, N, N-diethylaminomethyl, 2-fluorophenoxymethyl, 3-fluorophenoxy. Methyl, 4-fluorophenoxymethyl, pyridin-4-yloxymethyl, 2,4,6-trifluorophenoxy-methyl, 2-oxopyridin-1-ylmethyl, 2,2,2-trifluoroethoxy-methyl, 4 -Imidazol-1-ylphenoxy-methyl, 4- [1.2.4] -triazin-1-yl-phenoxymethyl, 2-phenylethyl, 3-hydroxypropyloxymethyl, 2-methoxyethyloxymethyl, pyrrolidine- 1-ylmethyl, piperidin-1-ylmethyl, 4-trifluoromethyl-piperidine 1-ylmethyl, 4-methylpiperazin-1-ylmethyl, 3,3,3-trifluoropropyloxymethyl, 4-fluorophenylthiomethyl, 4-fluorophenylsulfinylmethyl, 4-fluorophenylsulfonylmethyl, 2- (3 -Trifluoromethoxyphenylethyl)-, N-methyl-N-benzyl-aminomethyl, N-methyl-N-2-phenylethylaminomethyl, 3-hydroxypropylthiomethyl, 3-hydroxypropylsulfinyl-methyl, 3- Hydroxypropylsulfonylmethyl, N-methyl-N-2-indol-3-ylethylaminomethyl, 2- (4-trifluoromethylphenyl) ethyl, N-hydroxyaminocarbonylmethylaminomethyl, or 2-carboxyethylamino- Place with methyl It is.

In some embodiments, Ar ² is benzofuran-2-yl and the 5-position is 1-cyclopropylpiperidin-4-yloxy, piperidin-4-yloxy, tetrahydropyran-4-yloxy, 2, Substituted with 2,2-trifluoroethoxy, 2-pyrrolidin-1-ylethyloxy, or 1- (2,2,2-trifluoroethyl) piperidin-4-yloxy.

In some embodiments, Ar ² is 7-chloro-4-methylbenzofuran-2-yl, 4-methyl-benzofuran-2-yl, 7-fluoro-4-methylbenzofuran-2-yl, or 7- Fluoro-4-phenoxymethylbenzofuran-2-yl.

In some embodiments, Ar ² is thiophen-2-yl, pyridin-3-yl, 5-phenylthiophen-2-yl, quinolin-6-yl, 4-phenylthiazol-2-yl, benzothiazol- 2-yl, benzoxazol-2-yl, furan-2-yl, 1H-benzimidazol-2-yl, 1H-pyrrol-2-yl, 4- (pyridin-4-yl) -thiazol-2-yl, 1H-indol-5-yl, 1H-indol-3-yl, quinolin-3-yl, quinolin-8-yl, 1H-indazol-3-yl, 1H-benzotriazol-5-yl, isoquinolin-1-yl , Isoquinolin-3-yl, quinoxalin-2-yl, quinolin-2-yl, 1H-benzimidazol-5-yl, 1-methyl-indole- 3-yl, 4-MeO-quinolin-2-yl, quinolin-4-yl, 4-hydroxyquinolin-2-yl, pyridin-2-yl, 3-hydroxypyridin-2-yl, 6-hydroxypyridin-2 -Yl, 6- (4-nitrophenoxy) pyridin-2-yl, 4- (2-methoxyethoxy) quinolin-2-yl, 4- (2-dimethylaminoethoxy) quinolin-2-yl, 6-bromopyridine 2-yl, 5-bromopyridin-3-yl, 4-methoxyquinolin-2-yl, 5-phenylpyridin-3-yl, 6-benzyloxypyridin-2-yl, 6- (2-methylpropyloxy)- Pyridin-2-yl, 6- (2-phenylethyloxy) pyridin-2-yl, 4- (3,3,3-trifluoropropyloxy) quinolin-2-yl, 5 Thiophen-3-ylpyridin-3-yl, 6- (4-acetylaminophenoxy) -pyridin-2-yl, 6- (4-aminophenoxy) -pyridin-2-yl, or 5- (4-dimethylaminophenyl) ) Pyridin-3-yl.

V. Group V of compounds of formula (I) is a group of compounds wherein Ar ² is heteroaryl. In some embodiments, Ar ² is heteroaryl, optionally alkyl, halo, haloalkyl, alkoxy, alkoxyalkyl, hydroxyalkoxy, hydroxyalkoxyalkyl, alkoxyalkyloxy, alkoxyalkyloxyalkyl, aminoalkyl, Aminoalkoxy, haloalkoxy, haloalkoxyalkyl, optionally substituted phenylalkyl, optionally substituted phenyloxyalkyl, optionally substituted heteroaryl, optionally substituted heteroaralkyloxy, optionally substituted hetero Aryloxyalkyl, optionally substituted heterocycloalkylalkyl, optionally substituted heterocycloalkyloxy, optionally substituted heterocycloalkylalkyloxy, -alkylene-S ( O) _n R ^a (wherein n is 0-2 and R ^a is hydroxyalkyl or optionally substituted phenyl), -alkylene-NR ^e -alkylene CONR ^c R ^d (where R is ^c is hydroxyl and R ^d and R ^e are independently hydrogen or alkyl), or are substituted with one or two substituents independently selected from carboxyalkylaminoalkyl.

In some embodiments, Ar ² is thiophen-2-yl, pyridin-3-yl, quinolin-6-yl, benzothiazol-2-yl, benzoxazol-2-yl, benzofuran-2-yl, benzofuran- 5-yl, benzothien-2-yl, furan-2-yl, 1H-benzimidazol-2-yl, 1H-pyrrol-2-yl, thiazol-2-yl, 1H-indol-2-yl, 1H-indole -5-yl, 1H-indol-3-yl, quinolin-3-yl, quinolin-8-yl, 1H-indazol-3-yl, 1H-benzotriazol-5-yl, isoquinolin-1-yl, isoquinoline- 3-yl, quinoxalin-2-yl, quinolin-2-yl, 1H-benzimidazol-5-yl, quinolin-1-yl, pi Lysine-2-yl, pyridin-2-yl, quinolin-2-yl, furan-3-yl, thiophen-2-yl, or thiophen-3-yl. In some embodiments, Ar ² is benzofuran-2-yl or benzothien-2-yl, which are optionally substituted with one or two substituents as described in the immediately preceding paragraph. Yes.

In some embodiments, Ar ² is benzofuran-2-yl and is monosubstituted at the 3-position, 4-position or 5-position, or disubstituted at the 4-position and 7-position. In some embodiments, the benzofuran-2-yl at Ar ² is monosubstituted at the 3- or 5-position with a substituent described in the immediately preceding paragraph. In some embodiments, the substituents are independently chloro, fluoro, trifluoromethyl, methylethyl, methoxy, 1-cyclopropylpiperidin-4-yloxy, l- (2,2,2-trifluoroethyl ) Piperidin-4-yloxy, N, N-dimethylaminomethyl, N, N-diethylaminomethyl, 2-methoxyethoxymethyl, phenoxymethyl, 2-methoxyethoxy, 2-morpholin-4-ylethoxy, pyridine-3-methoxy, 2-hydroxyethoxy, 2-N, N-dimethylaminoethoxy, methoxymethyl, 3-i-propoxymethyl, morpholin-4-ylmethyl, 3-hydroxypropyloxymethyl, 2-fluorophenoxymethyl, 3-fluorophenoxymethyl, 4-fluorophenoxy-methyl, 3- Toxipropyloxymethyl, pyridin-4-yloxymethyl, 2,4,6-trifluorophenoxymethyl, 2-oxopyridin-1-ylmethyl, 2,2,2-trifluoroethoxymethyl, 4-imidazol-1- Irphenoxymethyl, 4- [l. 2.4-triazin-1-ylphenoxymethyl, 2-phenylethyl, pyrrolidin-1-ylmethyl, piperidin-1-ylmethyl, 4-trifluoromethylpiperidin-1-ylmethyl, 4-methylpiperazin-1-ylmethyl, 3 , 3,3-trifluoropropyloxymethyl, 4-fluorophenylthiomethyl, 4-fluorophenylsulfinylmethyl, 4-fluorophenylsulfonylmethyl, pyridin-3-ylmethyloxymethyl, tetrahydropyran-4-yloxy, 2, 2,2-trifluoroethyloxy, 2-pyrrolidin-1-ylethyloxy, piperidin-4-yloxy, N-methyl-N-benzylaminomethyl, N-methyl-N-2-phenylethylaminomethyl, 3- Hydroxypropylthiomethyl, 3 Hydroxypropylsulfinylmethyl, 3-hydroxypropylsulfonyl-methyl, N-methyl-N-2-indol-3-ylethylaminomethyl, 2- (4-trifluoromethylphenyl) ethyl, 2- (3-trifluoromethoxy Phenyl) ethyl, N-hydroxyaminocarbonyl-methylaminomethyl, or 3- (2-carboxyethylaminomethyl).

In some embodiments, Ar ² is benzofuran-2-yl and the 3-position is N 2 _, N-dimethylaminomethyl, N, N-diethylaminomethyl, 2-fluorophenoxymethyl, 3-fluorophenoxymethyl. 4-fluorophenoxy-methyl, pyridin-4-yloxymethyl, 2,4,6-trifluorophenoxymethyl, 2-oxopyridin-1-ylmethyl, 2,2,2-trifluoroethoxy-methyl, 4- Imidazol-1-ylphenoxy-methyl, 4- [1.2.4] -triazin-1-ylphenoxymethyl, 2-phenylethyl, 3-hydroxypropyloxymethyl, 2-methoxyethyloxymethyl, pyrrolidine-1- Ylmethyl, piperidin-1-ylmethyl, 4-trifluoromethyl-piperidine-1 Ilmethyl, 4-methylpiperazin-1-ylmethyl, 3,3,3-trifluoropropyloxymethyl, 4-fluorophenylthiomethyl, 4-fluorophenylsulfinylmethyl, 4-fluorophenylsulfonylmethyl, 2- (3-tri Fluoromethoxyphenylethyl)-, N-methyl-N-benzylaminomethyl, N-methyl-N-2-phenylethylaminomethyl, 3-hydroxypropylthiomethyl, 3-hydroxypropylsulfinyl-methyl, 3-hydroxypropylsulfonyl With methyl, N-methyl-N-2-indol-3-ylethylaminomethyl, 2- (4-trifluoromethylphenyl) ethyl, N-hydroxyaminocarbonyl-methylaminomethyl, or 2-carboxyethylamino-methyl Replace It has been.

In some embodiments, Ar ² is benzofuran-2-yl and the 5-position is cyclopropylpiperidin-4-yloxy, piperidin-4-yloxy, tetrahydropyran-4-yloxy, 2,2,2 -Substituted with trifluoroethoxy, 2-pyrrolidin-1-ylethyloxy, or 1- (2,2,2-trifluoroethyl) piperidin-4-yloxy.

In some embodiments, Ar ² is 7-chloro-4-methylbenzofuran-2-yl, 4-methylbenzofuran-2-yl, 7-fluoro-4-methylbenzofuran-2-yl, or 7-fluoro. -4-phenoxymethylbenzofuran-2-yl.

In some embodiments, Ar ² is thiophen-2-yl, pyridin-3-yl, 5-phenylthiophen-2-yl, quinolin-6-yl, 4-phenylthiazol-2-yl, benzothiazole 2 -Yl, benzoxazol-2-yl, furan-2-yl, 1H-benzimidazol-2-yl, 1H-pyrrol-2-yl, 4- (pyridin-4-yl) -thiazol-2-yl, 1H -Indol-5-yl, 1H-indol-3-yl, quinolin-3-yl, quinolin-8-yl, 1H-indazol-3-yl, 1H-benzotriazol-5-yl, isoquinolin-1-yl, Isoquinolin-3-yl, quinoxalin-2-yl, quinolin-2-yl, 1H-benzimidazol-5-yl, 1-methyl-indole-3- Yl, 4-MeO-quinolin-2-yl, quinolin-4-yl, 4-hydroxyquinolin-2-yl, pyridin-2-yl, 3-hydroxypyridin-2-yl, 6-hydroxypyridin-2-yl , 6- (4-Nitrophenoxy) pyridin-2-yl, 4- (2-methoxyethoxy) quinolin-2-yl, 4- (2-dimethylaminoethoxy) quinolin-2-yl, 6-bromopyridin-2 -Yl, 5-bromopyridin-3-yl, 4-methoxyquinolin-2-yl, 5-phenylpyridin-3-yl, 6-benzyloxypyridin-2-yl, 6- (2-methylpropyloxy)- Pyridin-2-yl, 6- (2-phenylethyloxy) pyridin-2-yl, 4- (3,3,3-trifluoropropyloxy) quinolin-2-yl, 5 Thiophen-3-ylpyridin-3-yl, 6- (4-acetylaminophenoxy) -pyridin-2-yl, 6- (4-aminophenoxy) -pyridin-2-yl, or 5- (4-dimethylaminophenyl) ) Pyridin-3-yl.

  Among the above groups II, III, IV and V, and groups described therein, in some embodiments, Y is a linear alkylene. In some embodiments, Y is ethylene or n-propylene. In some embodiments, Y is ethylene.

Among the above groups II, III, IV and V, and groups described therein, in some embodiments, Y is a branched alkylene. In some embodiments, Y _{is, -CH (C 2 H 5)} CH 2 -, - CH (i-C 3 H 7) CH 2 -, or -CH _(CH 3) CH ₂ - and A, The stereochemistry at the chiral carbon is (S). In some embodiments, Y is —CH (C ₂ Hs) CH ₂ —.

Among the above groups II, III, IV and V, and groups described therein, in some embodiments, Y is —CH ₂ CH (CH ₃ ) — and the stereochemistry at the chiral carbon. Is (R).

Among the above groups II, III, IV and V, and groups described therein, in some embodiments, Y is —CH (CH ₂ R ′) CH ₂ — or —CH (CH ₂ CH _{2 R} ') CH _{2 -} (in the formula, R' is alkylthio, alkylsulfonyl, optionally substituted phenylalkylthio, optionally substituted phenyl alkylsulfonyl, hydroxy, or optionally substituted phenoxy), is there. In some embodiments, R ′ is phenyl, phenoxy, 4-chlorophenyl, cyclohexyl, benzylthio, benzylsulfonyl, methylthio, methylsulfonyl, or hydroxy.

VI. The group VI of compounds of formula (I) is wherein X is —O—, R ¹ and R ³ are hydrogen, Ar ¹ is phenylene, Ar ² is aralkenyl, and Y is branched. Alkylene, -CONHOH and X are a group of compounds in the 1- or 4-position of the phenylene ring. In some embodiments, Ar ² is trans-phenyl-CH═CH—, wherein phenyl is optionally selected from one or two independently selected from alkyl, alkoxymethylenedioxy, or hydroxyl. Substituted with a substituent).

  The range of terms included in the above groups II to VI is as defined in the definition section of this specification.

References to the embodiments described above are intended to include all combinations of specific groups, unless otherwise specified.
General synthesis

  In one embodiment, a compound having the structure of formula (A) or formula (I) is produced by the method shown in the following reaction scheme. US Patent Application Publication No. 2005/0187261 describes a method for preparing hydroxamates, which is incorporated herein by reference.

  Starting materials and reagents used in the preparation of these compounds were obtained from commercial suppliers such as Aldrich Chemical (Milwaukee, Wis.), Bachem (Torrance, Calif.), Or Sigma (St. Louis, Mo.). Fieser and Fieser's Reagents for Organic Synthesis, Volumes 1-17 (John Wiley and Sons, 1991), Rodd's Chemistry of Carbon Volumes 1 to 17 1989), Organic Reactions, Volumes 1-40 (John Wiley and Sons). , 1991), published in March's Advanced Organic Chemistry, (John Wiley and Sons, Volume 4) and published in Larock's Comprehensive Organic Transforms (referenced by VCH Public 9). Generated by the method. These schemes are merely exemplary of some methods of synthesizing compounds of formula (A) or formula (I), and in some embodiments various modifications of these schemes are made. .

  In other embodiments, reaction starting materials and intermediates are isolated and purified using conventional techniques, including, but not limited to, filtration, distillation, crystallization, chromatography, and the like. . In other embodiments, such materials are characterized using conventional methods including physical constants and spectral data.

  Unless stated to the contrary, the reactions described herein can be performed at a temperature range of about −78 ° C. to about 150 ° C., about 0 ° C. to about 125 ° C., or about room temperature (or ambient temperature), such as It occurs at atmospheric pressure over about 20 ° C.

Formula (I) wherein X is —O— or —S (O) _n —, where n is 0 to 2, and other groups are described herein and in some embodiments. Is prepared according to the procedure shown and described in Scheme A below.

A compound of formula 1 wherein R is alkyl, X is —O— or —S—, and Ar ¹ is as defined herein; and formula 2 wherein PG is Reaction of a suitable amino protecting group) with an amino alcohol provides a compound of formula 3. The reaction is carried out in the presence of triphenylphosphine and diisopropyl azodicarboxylate in a suitable organic solvent such as tetrahydrofuran furan.

Compounds of formula 1 such as methyl 4-hydroxybenzoate, methyl 4-mercaptobenzoate, and methyl 3-hydroxyisoxazole-5-carboxylate are commercially available. In some embodiments, a compound of formula 2 is reacted from a commercially available amino alcohol with an amine with a suitable amino protecting group such as benzyloxycarbonyl, tert-butoxycarbonyl, and the like, under suitable reaction conditions. Prepare by. In some embodiments, T.P. W. Greene, Protecting Groups in Organic Synthesis, John Wiley & Sons, Inc. 1981 provides a detailed description of suitable amino protecting groups and reaction conditions for preparing them, the list of suitable amino protecting groups and reaction conditions being incorporated herein by reference. Amino alcohols such as 2-ethanolamine, 2-amino-1-propanol, 2-methylaminoethanol, 2-amino-2-methyl-1-propanol, 2-amino-1-propanol, 4-amino-2 -Butanol and 1-amino-2-butanol are commercially available. In one embodiment, the compound of formula 2 is protected from a commercially available amino acid by protecting the amino group with a suitable protecting group and then using an appropriate reducing agent to reduce the acid group to a hydroxy group under standard conditions. To prepare. In some embodiments where X of the compound of formula (I) is —SO ₂ —, the corresponding compound of formula 3 (wherein X is —S—) is OXONE®, m-chloroperoxide. Treat with an oxidizing agent such as benzoic acid.

  Removal of the amino protecting group of 3 gives the compound of formula 4. The reaction conditions used to remove the amino protecting group depend on the nature of the protecting group. For example, in some embodiments where the protecting group is tert-butoxycarbonyl, it is removed under acid reaction conditions. Suitable acids are trifluoroacetic acid, hydrochloric acid and the like in a suitable organic solvent such as methanol, dioxane, tetrahydrofuran furan and the like. In some embodiments where the protecting group is benzyl or benzyloxycarbonyl, it is removed under catalytic hydrogenation reaction conditions. Suitable catalysts are platinum based catalysts and other suitable catalysts. In other embodiments, other suitable reaction conditions for their elimination are described in T.W. W. Greene, Protecting Groups in Organic Synthesis, John Wiley & Sons, Inc. 1981. The reaction is carried out in an inert organic solvent methylene chloride, tetrahydrofuran furan, dioxane or the like.

Reaction of 4 with an acid or acid derivative (eg, acid chloride) of the formula: Ar ² —COZ, where Z is hydroxy or halo, provides a compound of formula 5. Again, the reaction conditions used depend on the nature of the Z group. In some embodiments where Z is hydroxy, the reaction is usually carried out with a suitable coupling agent such as benzotriazol-1-yloxytrispyrrolidino-phosphonium hexafluorophosphate (PyBOP®), O— Benzotriazol-1-yl-N, N, N ′, N′-tetramethyl-uronium hexafluorophosphate (HBTU), O- (7-azabenzotriazol-1-yl) -1,3,3 Optionally in the presence of tetramethyluronium hexafluorophosphate (HATU), l- (3-dimethylaminopropyl) -3-ethylcarbodiimide hydrochloride (EDC.HCl), or 1,3-dicyclohexylcarbodiimide (DCC) 1-hydroxybenzotriazole hydrate (HOBt-H ₂ O), And in the presence of a base such as N, N-diisopropylethylamine, triethylamine, N-methylmorpholine and the like. In some embodiments, the reaction is performed at about 20-30 ° C. In some embodiments, the reaction is conducted at about 25 ° C. and requires about 2 to about 24 hours to complete. Suitable reaction solvents are inert organic solvents such as halogenated organic solvents (eg methylene chloride, chloroform, etc.), ethereal solvents such as acetonitrile, N, N-dimethylformamide, tetrahydrofuran, dioxane, and the like. In some embodiments, the reaction is conducted, dichloromethane or N, N- _{dimethylformamide,} with HOBt-H 2 O, EDC- HCl.

When Ar ² —COZ is an acid halide, the reaction is performed in the presence of a suitable base (eg, triethylamine, diisopropylethylamine, pyridine, etc.). Suitable reaction solvents are polar organic solvents such as tetrahydrofuran, acetonitrile, N, N-dimethylformamide (DMF), dichloromethane, or any suitable mixture thereof. In a further embodiment, acid halides such as acid chlorides are prepared by reacting the corresponding acid with a halogenating agent such as oxalyl chloride, thionyl chloride, phosphorus oxychloride and the like. In yet a further embodiment, the formula: acid Ar ² -COZ is commercially available, or prepared by standard methods from commercially available starting materials. For example, benzoic acid, cinnamic acid, phenylacetic acid, nicotinic acid, isonicotinic acid, 3-methylbenzofuran-2-carboxylic acid and benzofuran-2-carboxylic acid are commercially available. Others such as 3-phenoxymethylbenzofuran-2-carboxylic acid are first converted from commercially available 3-methylbenzofuran-2-carboxylic acid to 2-bromomethylbenzofuran-2-carboxylic acid (standard It is easily produced by bromination with N-bromosuccinimide under conditions) and then reaction with phenol. In other embodiments, compound 5 (wherein R ³ is hydrogen) is optionally reacted under standard alkylation conditions with an alkylating agent to provide the corresponding compound of formula 5 ( Where R ³ is other than hydrogen).

Compound 5 is then converted to a compound of formula (I) by reaction with aqueous hydroxylamine in the presence of a base such as sodium hydroxide and a mixture of organic solvents such as tetrahydrofuranfuran and methanol. In one embodiment, first, the fifth group, in a suitable organic solvent such as dimethyl formamide, optionally in the presence of l- hydroxybenzotriazole hydrate _{(HOBt-H 2 O),} l- ( Activated with a suitable coupling agent such as 3-dimethylaminopropyl) -3-ethylcarbodiimide hydrochloride (EDC-ΗC1) or 1,3-dicyclohexylcarbodiimide (DCC), then N, N-diisopropylethylamine, triethylamine, Reaction with hydroxylamine hydrochloride in the presence of a base such as N-methylmorpholine. In other embodiments, a compound of formula (I) is prepared from compound 5 by the method disclosed in US Pat. No. 5,998,412 (the method of preparation of which is incorporated herein by reference). To do.

In yet a further embodiment, the compound of formula (I) is converted to another compound of formula (I). For example, formula (I) (wherein Ar ¹ is phenylene, X is —O—, Y is ethylene, Ar ² is 3-dimethylaminomethyl-benzofuran-2-yl, R ¹ And R ³ is hydrogen) is a compound of formula 4 wherein Ar ¹ is phenylene, X is —O—, Y is ethylene, and R is alkyl. - by reacting as described above and methylbenzofuran-2-carboxylic acid, (wherein, Ar ² is 3-methylbenzofuran-2-yl) equation 5 is prepared by obtaining a compound of. Bromination of the methyl group with a suitable brominating agent such as N-bromosuccinimide followed by reaction with dimethylamine gives the corresponding 3-dimethylaminobenzofuran-2-yl compound, which is then described above. Conversion to the desired compound under the reaction conditions given.
Administration and pharmaceutical composition

  In general, a compound having the structure of formula (A) or formula (I) is administered in a therapeutically effective amount by any mode permitted for the administration of agents that provide similar benefits. The actual amount of the compound of formula (A) or formula (I), ie the active ingredient, depends on the severity of the disease, injury or condition to be treated, the age of the subject and the associated health condition, the effectiveness of the compound used, A number of factors will depend on the route and form of administration, and other factors.

  In one embodiment, the pharmaceutical composition is used using one or more physiologically acceptable carriers that include excipients and adjuvants that facilitate processing of the active compound into a pharmaceutical use formulation. Formulate by conventional methods. Proper formulation depends on the route of administration chosen. For an overview of the pharmaceutical compositions described herein, see, for example, Remington: The Science and Practice of Pharmacy, Nineteenth Ed (Easton, Pa .: Mack Publishing Company, 1995), Hoover, John E. et al. , Remington's Pharmaceutical Sciences, Mack Publishing, Easton, Pennsylvania 1975, Liberman, H .; A. And Lachman, L .; Eds. , Pharmaceutical Dosage Forms, Marcel Decker, New York, N .; Y. , 1980, and Pharmaceutical Dosage Forms and Drug Delivery Systems, Seventh Ed. (Lippincott Williams & Wilkins 1999), a summary of which is incorporated herein by reference.

  In the present invention, a compound described herein, for example a compound of formula (A) or formula (I), and a pharmaceutically acceptable diluent (s), excipient (s), or A pharmaceutical composition comprising a carrier (s) is provided. Furthermore, the compounds described herein are administered as a pharmaceutical composition in which the compounds described herein described are mixed with other active ingredients, as in combination therapy. In some embodiments, the pharmaceutical composition comprises other pharmaceuticals or pharmaceutical formulations, carriers, adjuvants, such as preservatives, stabilizers, wetting or emulsifying agents, solubility enhancers, salts for controlling osmotic pressure, And / or contain a buffer. In other embodiments, the pharmaceutical composition also includes other therapeutically valuable substances.

  In certain embodiments, the composition comprises one or more pH adjusting or buffering agents, for example acids such as acetic acid, boric acid, citric acid, lactic acid, phosphoric acid and hydrochloric acid, sodium hydroxide, sodium phosphate, Also included are bases such as sodium borate, sodium citrate, sodium acetate, sodium lactate and tris-hydroxymethylaminomethane, buffers such as citric acid / dextrose, sodium bicarbonate and ammonium chloride. Such acids, bases and buffers are included in amounts required to keep the pH of the composition within an acceptable range.

  In other embodiments, the composition also includes one or more salts in an amount necessary to bring the osmotic pressure of the composition into an acceptable range. Such salts include salts containing sodium, potassium or ammonium cations and hydrochloric acid, citric acid, ascorbic acid, boric acid, phosphoric acid, hydrogen carbonate, sulfuric acid, thiosulfuric acid or bisulfite anions. Suitable salts include sodium chloride, potassium chloride, sodium thiosulfate, sodium bisulfite and ammonium sulfate.

  As used herein, a pharmaceutical composition comprises at least one compound described herein, such as a compound of formula (A) or formula (I), and other chemical components, such as carriers, stabilizers, Refers to mixtures with diluents, dispersants, suspensions, thickeners and / or excipients. The pharmaceutical composition facilitates administration of the compound to a living body. In practicing the methods of treatment or use provided herein, a therapeutically effective amount of a compound described herein is administered to a mammal suffering from a disease, disorder or condition to be treated in a pharmaceutical composition. In some embodiments, the mammal is a human. A therapeutically effective amount will vary widely depending on the severity of the disease, disorder or condition, the age and associated health of the subject, the potency of the compound used, and other factors. In some embodiments, the compounds are used alone or in combination with one or more therapeutic agents as a component of a mixture.

  In other embodiments, the pharmaceutical formulations described herein are administered via oral, parenteral (eg, intravenous, subcutaneous, intramuscular), buccal mucosa, topical, transanal or transdermal routes of administration (including those). Administered to a subject by multiple routes of administration, including but not limited to. The pharmaceutical formulations described herein include aqueous liquid dispersions, self-emulsifying dispersions, solid solutions, liposome dispersions, aerosols, solid dosage forms, powders, immediate release formulations, controlled release formulations, immediate melt formulations, tablets, Capsules, pills, delayed release formulations, sustained release formulations, pulsatile release formulations, multiparticulate formulations, and mixed immediate and controlled release formulations include, but are not limited to.

  In other embodiments, a pharmaceutical composition comprising a compound described herein is a conventional method such as, for example, conventional mixing, dissolving, granulating, dragee forming, powdering, emulsifying, Manufactured by an encapsulation, encapsulation or compression process.

  The pharmaceutical composition comprises at least one compound described herein as an active ingredient, for example a compound of formula (A) or formula (I), in free acid or free base form, or pharmaceutically acceptable. Contains in salt form. Furthermore, the methods and pharmaceutical compositions described herein also include the use of N-oxides, crystalline forms (also known as polymorphs), and active metabolites of these compounds with the same type of activity. In some embodiments, compounds of formula (A) or formula (I) exist as tautomers. All tautomers are included within the scope of the compounds presented herein. Further, in some embodiments, the compounds described herein exist in unsolvated forms and in solvated forms with pharmaceutically acceptable solvents such as water, ethanol, and the like. The solvated forms of the compounds presented herein are also considered to be disclosed herein.

“Bioavailability” refers to the percent of the weight of a compound disclosed herein, such as a compound of formula (A) or formula (I), delivered to the systemic circulation of the animal or human being tested. . The total drug exposure (AUC _(0-∞) ) when administered intravenously is usually defined as 100% availability (F%). “Oral bioavailability” refers to a compound disclosed herein, such as a compound of formula (A) or formula (I), when the pharmaceutical composition is taken orally as compared to by intravenous injection. The degree to which it is absorbed by the systemic circulation.

“Plasma concentration” refers to the concentration of a compound disclosed herein, such as a compound of formula (A) or formula (I), in the plasma component of the blood of a subject. In some embodiments, the plasma concentration of a compound of formula (A) or formula (I) may vary greatly between subjects due to variations in metabolism and / or possible interactions with other therapeutic agents. It will be understood. According to one embodiment disclosed herein, the plasma concentration of the compound of formula (A) or formula (I) varies from subject to subject. Similarly, in another embodiment, the maximum plasma concentration (C _max ) or the time to reach maximum plasma concentration (T _max ), or the total area under the plasma concentration time curve (AUC _(0−∞) ) The value varies from subject to subject. Because of these variations, in other embodiments, the amount required to constitute a “therapeutically effective amount” of a compound of formula (A) or formula (I) will vary from subject to subject.

  “Drug absorption” or “absorption” generally refers to the process of drug movement from the site of drug administration through the protective wall to the blood vessel or site of action, eg, the drug from the gastrointestinal tract to the portal vein or lymphatic system. Say movement.

  “Measurable serum concentration” or “Measurable plasma concentration” was generally measured as mg, μg or ng of therapeutic agent per ml, 1 dl or 1 liter of serum absorbed into the bloodstream after administration. List serum or plasma concentrations. As used herein, measurable plasma concentrations are generally measured in ng / ml or μg / ml.

  “Pharmacodynamics” refers to factors that determine the observed biological response to drug concentration at the site of action.

  “Pharmacokinetics” refers to the factors that determine the achievement and maintenance of the proper concentration of drug at the site of action.

  As used herein, “steady state” refers to the amount of drug administered being equal to the amount of drug removed within a dosing interval, resulting in a plateau or constant plasma drug exposure.

As used herein, the term “subject” is used to mean an animal, such as a mammal, including a human or non-human. In some embodiments, the terms patient and subject are used interchangeably. In further embodiments, the pharmaceutical compositions used herein comprising a compound of formula (A) or formula (I) are to be orally digested by any suitable dosage form, eg, the patient being treated. Aqueous oral dispersions, liquids, gels, syrups, elixirs, slurries, suspensions, solid oral dosage forms, aerosols, controlled release formulations, immediate melt formulations, effervescent formulations, lyophilized formulations, tablets, powders Pills, dragees, capsules, delayed release formulations, sustained release formulations, pulsatile release formulations, multiparticulate formulations, and mixed immediate release and controlled release formulations (but not limited to).
Examples of dosing methods and treatment regimens

  In one aspect, a composition comprising a compound (s) described herein is administered for prophylactic and / or therapeutic measures. In therapeutic applications, a patient already suffering from a disease, disorder or condition is administered an amount of the composition sufficient to cure or at least partially abate the symptoms of the disease, disorder or condition. Effective amounts for this application will depend on the severity and course of the disease, disorder or condition, previous treatment, patient health, weight and response to medication, and the judgment of the attending physician.

  For prophylactic applications, a composition comprising a compound described herein is administered to a patient who is highly sensitive to or otherwise at risk for a particular disease, disorder or condition. Such an amount is defined as a “prophylactically effective amount or dose”. Again, the exact amount depends on the patient's health, weight, etc. In some embodiments, when used on a patient, an effective amount for this use is the severity and course of the disease, disorder or condition, prior treatment, patient health and response to drugs, and Depends on doctor's judgment.

  In some embodiments, if the patient's condition does not improve, the administration of the compound chronically, i.e., to reduce or control or limit the symptoms of the patient's disease, disorder or condition at the discretion of the physician For long periods of time, for example, while the patient is alive.

  In some embodiments, if the patient's condition improves, the compound may be administered continuously at the discretion of the physician, or the dose of drug administered may be temporarily reduced for a period of time. Or temporarily stop (ie, “drug holiday”). In other embodiments, the length of the drug holiday varies between 2 days and 1 year, and by way of example only, about 2 days, about 3 days, about 4 days, about 5 days, about 6 days. About 7 days, about 10 days, about 12 days, about 15 days, about 20 days, about 28 days, about 35 days, about 50 days, about 70 days, about 100 days, about 120 days, about 150 days, About 180 days, about 200 days, about 250 days, about 280 days, about 300 days, about 320 days, about 350 days, or about 365 days. In a further embodiment, the dose reduced during the drug holiday is about 10% to about 100%, by way of example only, about 10%, about 15%, about 20%, about 25%, about 30%, about 30%, 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95% Or about 100%.

  If the patient's condition improves, a maintenance dose is administered if necessary. Subsequently, in other embodiments, the dose or number of administrations, or both, is reduced to a level that maintains the improved disease, disorder or condition, depending on the symptoms. However, in a further embodiment, the patient will require intermittent treatment on a long-term basis upon any recurrence of symptoms.

  In other embodiments, the amount of a drug corresponding to such an amount is such as the particular compound, disease, disorder or condition and its severity, the individuality (eg, body weight) of the subject or host in need of treatment. Specific circumstances surrounding the case, such as the drug being administered, the route of administration, the condition being treated, and the subject or host being treated It is determined on a daily basis by a method according to. However, in some embodiments, dosages used to treat human adults are typically in the range of about 0.02 to about 5000 mg / day or about 1 to about 1500 mg / day. In further embodiments, the desired dose is a single dose, or simultaneously (or in a short time) or at appropriate intervals, eg, twice, three times, four times or more per day. For convenience, it is presented in divided doses.

  In some embodiments, the pharmaceutical compositions described herein take unit dosage forms suitable for single administration of precise dosages. In unit dosage form, the formulation is divided into unit doses containing appropriate quantities of one or more compound. In other embodiments, the unit dosage is in the form of a package containing discrete amounts of the formulation. Non-limiting examples include packaged tablets or capsules, and powders in vials or ampoules. In another embodiment, the aqueous suspension composition is in a single dose, non-closable container. In a further embodiment, multiple doses of closable containers are used, in which case it is common to include a preservative in the composition. By way of example only, formulations for parenteral injection are presented in unit dosage forms, including but not limited to ampoules, or presented with preservatives added in multi-dose containers. .

  A suitable daily dosage for the compounds described herein described herein is from about 0.01 to about 2.5 mg / kg body weight. The indicated daily dose in large mammals, including but not limited to humans, is in the range of about 0.5 mg to about 100 mg, divided doses, for example up to 4 times per day (limited to this). Not conveniently) or in sustained release form. Suitable unit dosage forms for oral administration contain from about 1 to about 50 mg of active ingredient. Because the number of variables for a single treatment regimen is large, the above ranges are only suggestions and it is not uncommon to deviate significantly from these recommended values. In further embodiments, such dosages are numerous variables, the activity of the compound used, the disease to be treated, the disorder or condition, the mode of administration, the individual subject's requirements, the severity of the disease, the disorder being treated. Or depending on the condition and the judgment of the attending physician (but not limited to).

In a still further embodiment, the toxicity and therapeutic efficacy of such treatment regimes are measured by LD ₅₀ (dose that causes 50% of the population to die) and ED ₅₀ (dose that has a therapeutic effect in 50% of the population). Determined by standard pharmaceutical procedures in cell cultures or experimental animals, including but not limited to). The dose ratio between toxic and therapeutic effects is the therapeutic index and in some embodiments is expressed as the ratio between LD ₅₀ and ED ₅₀ . In other embodiments, data obtained from cell culture assays and animal studies are used to create a dose range for use in humans. In some embodiments, the dosage of such compounds is placed within a circulating concentration that includes the ED ₅₀ with minimal toxicity. In still further embodiments, the dosage varies within this range depending upon the dosage form employed and the route of administration utilized.
Combination treatment

  In general, in embodiments where combination therapy is used, the compositions described herein and other agents need not be administered in the same pharmaceutical composition, and in some embodiments, different physical Are administered by different routes due to chemical and chemical characteristics. In some embodiments, the first administration is made according to established protocols, and then the dosage and mode of administration and number of administrations are varied by those skilled in the art based on the observed effects.

  In some embodiments, the therapeutically effective dose varies when the agent is used in a therapeutic combination. In addition, combination treatment includes periodic treatments that start and stop at various times to assist in the clinical management of the patient. For the combination therapies described herein, the dosage of the compounds administered together will vary depending on the type of co-drug used, the particular drug used, the disease, disorder or condition being treated, etc.

  In some embodiments, the dosage regimen for treating, preventing or alleviating a condition sought to be alleviated will vary according to various factors. These factors include the disorder affected by the subject, as well as the age, weight, sex, diet and medical status of the subject. Thus, in other embodiments, the dosage regimen actually used varies greatly and thus deviates from the dosage regimen described herein.

  Combinations of compounds having the structure of formula (A) or formula (I) with other anticancer or chemotherapeutic agents are contemplated. In some embodiments, examples of such agents are Cancer Principles and Practice of Oncology, V.M. T.A. Devita and S.M. Hellman (Editor), 6th edition (February 15, 2001), Lippincott Williams & Wilkins Publishers. Such anticancer agents include, but are not limited to: Estrogen receptor modulator, androgen receptor modulator, retinoid receptor modulator, cytotoxic / cytostatic agent, antiproliferative agent, prenylprotein transferase inhibitor, HMG-CoA reductase inhibitor, nitrogen mustard, nitroso Urea, angiogenesis inhibitor, cell proliferation and survival signal pathway inhibitor, apoptosis inducer, drug that interferes with cell cycle checkpoint, drug that blocks receptor tyrosine kinase (RTK), integrin blocker, NSAID, PPAR agonist Inhibitors of inherent multidrug resistance (MDR), antiemetics, drugs useful for the treatment of anemia, drugs useful for the treatment of neutropenia, immunopotentiators, biphosphonates, aromatase inhibitors, neoplastic cells Γ-secretase, a drug containing a terminal differentiation inducer Harm agents, cancer vaccines, and any combination thereof.

  “Estrogen receptor modulators” refers to compounds that interfere with or inhibit the binding of estrogen to the receptor, regardless of mechanism. Examples of estrogen receptor modulators include tamoxifen, raloxifene, idoxifene, LY3533381, LY117081, toremifene, fulvestrant, 4- [7- (2,2-dimethyl-1-oxopropoxy-4-methyl-2- [4- [2- (1-piperidinyl) ethoxy] phenyl] -2H-1-benzopyran-3-yl] -phenyl-2,2-dimethylpropanoate, 4,4′-dihydroxybenzophenone-2,4-dinitrophenyl- Examples include, but are not limited to, hydrazone and SH646.

  In some embodiments, the estrogen receptor modulator is tamoxifen and raloxifene.

  “Androgen receptor modulator” refers to a compound that interferes with or inhibits binding of androgen to the receptor, regardless of mechanism. Examples of androgen receptor modulators include finasteride and other 5α-reductase inhibitors, nilutamide, flutamide, bicalutamide, liarozole and abiraterone acetate.

  “Retinoid receptor modulators” refers to compounds that interfere with or inhibit the binding of retinoids to the receptor, regardless of mechanism. Examples of such retinoid receptor modulators include bexarotene, tretinoin, 13-cis-retinoic acid, 9-cis-retinoic acid, α-difluoromethylornithine, ILX23-7553, trans-N- (4′-hydroxyphenyl) Retinamide, and N-4-carboxyphenylretinamide.

  "Cytotoxic / cytostatic agent" refers to a compound that causes cell death, inhibits cell growth primarily by directly interfering with cell function, or inhibits or interferes with cell mitosis, alkylating Agent, tumor necrosis factor, intervention, hypoxia activatable compound, microtubule inhibitor / microtubule stabilizer, mitotic kinesin inhibitor, histone deacetylase inhibitor, mitotic progression Involved kinase inhibitors, antimetabolites, biological response modifiers, hormone / antihormone therapeutics, hematopoietic growth factors, monoclonal antibody targeted therapeutics, topoisomerase inhibitors, proteasome inhibitors, and ubiquitin ligase inhibitors Can be mentioned.

  Examples of cytotoxic drugs include tirapazamine, sertenel, cachectin, ifosfamide, tasonermine, lonidamine, carboplatin, altretamine, prednimustine, dibromozulcitol, ranimustine, fotemustine, nedaplatin, oxaliplatin, temozolomide, heptaplatin, estramus Sulfantosylate, Trophosphamide, Nimustine, Dibrospidi chloride, Pumitepa, Lovaplatin, Satraplatin, Profilomycin, Profilomycin, Cisplatin, Irofulvene, Dexifostamide, M-Aminedichloro (2-methyl-pyridine) platinum, Benzylguanine , Glufosfamide, GPX100, (trans-, trans-, trans) -bis-mu- (hex -1,6-diamine) -mu- [diamine-platinum (II)] bis [diamine (chloro) platinum (II)]-tetrachloride, dialidinylspermine, arsenic trioxide, 1- (11-dodecyl) Amino-10-hydroxyundecyl) -3,7-dimethylxanthine, zorubicin, idarubicin, daunorubicin, bisantrene, mitoxantrone, pirarubicin, pinafide, valrubicin, amrubicin, antineoplaston, 3'-deamino-3'-morpholino- 13-deoxo-10-hydroxycarminomycin, annamycin, galarubicin, erinafide, MEN10755, and 4-demethoxy-3-deamino-3-aziridinyl-4-methylsulfonyl-daunorubicin (see WO 00/50032). Et That, but is not limited to these.

  Examples of microtubule inhibitors include paclitaxel, vindesine sulfate, 3 ′, 4′-didehydro-4′-deoxy-8′-norvin calleucoblastine, docetaxol, lysoxine, dolastatin, mibobrine isethionate, auristatin, Semadine, RPR109881, BMS184476, vinflunine, cryptophycin, 2,3,4,5,6-pentafluoro-N- (3-fluoro-4-methoxyphenyl) benzenesulfonamide, anhydrovinblastine, N, N-dimethyl- L-valyl-L-valyl-N-methyl-L-valyl-L-prolyl-L-proline-t-butylamide, TDX258, and BMS188797.

  Some examples of topoisomerase inhibitors include topotecan, hycaptamine, irinotecan, rubitecan, 6-ethoxypropionyl-3 ′, 4′-O-exo-benzylidene-chartoleucine, 9-methoxy-N, N-dimethyl. -5-nitropyrazolo [3,4,5-kl] acridine-2- (6H) propanamine, 1-amino-9-ethyl-5-fluoro-2,3-dihydro-9-hydroxy-4-methyl-1H, 12H-benzo [de] pyrano [3 ′, 4 ′: b, 7] -indolidino [1,2b] quinoline-10,13 (9H, 15H) dione, root tecan, 7- [2- (N-isopropylamino) Ethyl]-(20S) camptothecin, BNP1350, BNPI1100, BN80915, BN8 942, etoposide phosphate, teniposide, sobuzoxane, 2'-dimethylamino-2'-deoxy-etoposide, GL331, N- [2- (dimethylamino) ethyl] -9-hydroxy-5,6-dimethyl-6H-pyrido [4,3-b] carbazole-1-carboxamide, aslacrine, (5a, 5aB, 8aa, 9b) -9- [2- [N- [2- (dimethylamino) ethyl] -N-methylamino] ethyl] -5- [4-hydroxy-3,5-dimethoxyphenyl] -5,5a, 6,8,8a, 9-hexohydrofuro (3 ', 4': 6,7) cortic (2,3-d) -1 , 3-dioxol-6-one, 2,3- (methylenedioxy) -5-methyl-7-hydroxy-8-methoxybenzo [c] -phenanthridinium, 6,9-bis [ 2-aminoethyl) amino] benzo [g] isoquinoline-5,10-dione, 5- (3-aminopropylamino) -7,10-dihydroxy-2- (2-hydroxyethylaminomethyl) -6H-pyrazolo [ 4,5,1-de] acridin-6-one, N- [1- [2 (diethylamino) ethylamino] -7-methoxy-9-oxo-9H-thioxanthen-4-ylmethyl] formamide, N- ( 2- (dimethylamino) ethyl) acridine-4-carboxamide, 6-[[2- (dimethylamino) ethyl] amino] -3-hydroxy-7H-indeno [2,1-c] quinolin-7-one, and Dimesna is mentioned.

  “Antiproliferative agents” include antisense RNA and DNA oligonucleotides such as G3139, ODN698, RVASKRAS, GEM231, and INX3001, and antimetabolites such as enocitabine, carmoflu, tegafur, pentostatin, doxyfluridine, trimethrexate, Fludarabine, capecitabine, galocitabine, cytarabine ocphosphate, fosterabine sodium hydrate, raltitrexed, partitrexide, emiteflu, thiazofurin, decitabine, noratrexed, pemetrexed, nerzarabine, 2'-deoxycytidin Fluoromethylene-2′-deoxy-cytidine, N- [5- (2,3-dihydro-benzofuryl) sulfonate ] -N '-(3,4-dichlorophenyl) urea, N6- [4-deoxy-4- [N2- [2 (E), 4 (E) -tetradecadienoyl] glycylamino] -L-glycero-B -L-manno-heptopyranosyl] adenine, aplidine, etainacidin, troxacitabine, 4- [2-amino-4-oxo-4,6,7,8-tetrahydro-3H-pyrimidino [5,4-b] [1,4 ] Thiazin-6-yl- (S) -ethyl] -2,5-thienoyl-L-glutamic acid, aminopterin, 5-fluorouracil, alanosine, 11-acetyl-8- (carbamoyloxymethyl) -4-formyl-6 -Methoxy-14-oxa-1,11-diazatetracyclo (7.4.1.0.0) -tetradeca-2,4,6-trien-9-yl acetate Ter, swainsonine, lometrexol, dexrazoxane, methioninase, 2'-cyano-2'-deoxy-N4-palmitoyl-1-BD-arabinofuranosylcytosine, and 3-aminopyridine-2-carboxaldehyde Semicarbazone is mentioned. “Anti-proliferative agents” also include tumor suppressor genes, such as trastuzumab and p53, from monoclonal antibodies to growth factors, in addition to those listed below under “Angiogenesis inhibitors” Delivered by recombinant virus-mediated gene transfer).

  A “prenyl protein transferase inhibitor” refers to a compound that inhibits any one or any combination of prenyl protein transferases, such as farnesyl-protein transferase (FPTase), geranylgeranyl-protein transferase type I (GGPTase-I). ), And geranylgeranyl-protein transferase type II (GGPTase-II, also referred to as lab GGPTase). Examples of prenyl protein transferase inhibitors include (±) -6- [amino (4-chlorophenyl) (1-methyl-1H-imidazol-5-yl) methyl] -4- {3-chlorophenyl) -1-methyl -2 (1H) -quinolinone, (-)-6- [amino (4-chlorophenyl-1) (1-methyl-1H-imidazol-5-yl) methyl] -4- (3-chlorophenyl) -1-methyl -2 (1H) -quinolinone, (+)-6- [amino (4-chlorophenyl) (1-methyl-1H-imidazol-5-yl) methyl] -4- (3-chlorophenyl) -1-methyl-2 (1H) -Quinolinone, 5 (S) -n-butyl-1- (2,3-dimethyl-phenyl) -4- [l- (4-cyanobenzyl) -5-imidazolylmethyl] -2-pi Radinone, (S) -1- (3-chlorophenyl) -4- [1- (4-cyanobenzyl) -5-imidazolylmethyl J-5- [2- (ethanesulfonyl) -methyl) -2-piperazinone, 5 (S) -n-butyl-1- (2-methylphenyl) -4- [l- (4-cyanobenzyl) -5-imidazolylmethyl] -2-piperazinone, l- (3-chlorophenyl) -4 -[L- (4-cyanobenzyl) -2-methyl-5-imidazolylmethyl] -2-piperazinone, l- (2,2-diphenylethyl) -3- [N- (1- (4-cyanobenzyl) ) -1H-imidazol-5-ylethyl) carbamoyl] -piperidine, 4- {5- [4-hydroxymethyl-4- (4-chloropyridin-2-ylmethyl) -piperidin-1-ylmethyl ] -2-methylimidazol-1-ylmethyl} benzonitrile, 4- {5- [4-hydroxymethyl-4- (3-chlorobenzyl) -piperidin-1-ylmethyl] -2-methylimidazol-1-ylmethyl} Benzonitrile, 4- {3- [4- (2-oxo-2H-pyridin-1-yl) benzyl] -3H-imidazol-4-ylmethyl} benzonitrile, 4- {3- [4- (5-chloro 2-oxo-2H- [l, 2 ′] bipyridin-5′-ylmethyl] -3H-imidazol-4-ylmethyl} benzonitrile, 4- {3- [4- (2-oxo-2H- [1, 2 ′] bipyridin-5′-ylmethyl] -3H-imidazol-4-ylmethyl} benzonitrile, 4- [3- {2-oxo-1-phenyl-1,2-dihydropyridine 4-ylmethyl) -3H-imidazol-4-ylmethyl} benzonitrile, 18,19-dihydro-19-oxo-5H, 17H-6,10: 12,16-dimeteno-1H-imidazo [4,3-c] [L, 11,4] dioxa-azacyclononadecin-9-carbonitrile, (±) -19,20-dihydro-19-oxo-5H-18,21-ethano-12,14-etheno-6,10 -Metheno-22H-benzo [d] imidazo [4,3-k] [1,6,9,12] -oxatriaza-cyclooctadecin-9-carbonitrile, 19,20-dihydro-19-oxo-5H, 17H-18,21-Etano-6,10: 12,16-Dimetheno-22H-imidazo [3,4-h] [1,8, ll, 14] oxatriazacyclo-eicosine-9 -Carbonitrile and (±) -19,20-dihydro-3-methyl-19-oxo-5H-18,21-ethano-12,14-etheno-6,10-metheno-22H-benzo [d] imidazo [4,3-k] [l, 6.9,12] oxatriazacyclooctadecin-9-carbonitrile.

  “HMG-CoA reductase inhibitors” refers to inhibitors of 3-hydroxy-3-methylglutaryl-CoA reductase. In some embodiments, compounds that are inhibitory to HMG-CoA reductase are readily identified using known assays. The terms “HMG-CoA reductase inhibitor” and “inhibitor of HMG-CoA reductase” have the same meaning when used herein.

  In some embodiments, examples of HMG-CoA reductase inhibitors include lovastatin (MEVACOR®), simvastatin (ZOCOR®), pravastatin (PRAVACOL®), fluvastatin (LESCOL ( Registered trademark)), atorvastatin (LIPITOR®) and ceivastatin (also known as rivastatin and BAYCHOL®), but are not limited to these. In some embodiments, the structural formula of these and additional HMG-CoA reductase inhibitors used in the method are M. Yalpani, “Cholesterol Lowering Drugs”, Chemistry & Industry, pp. 85-89 (February 5, 1996), and in U.S. Pat. Nos. 4,782,084 and 4,885,314. As used herein, the term HMG-CoA reductase inhibitor refers to all pharmaceutically acceptable lactone and open acid forms (ie, when the lactone ring is opened to form the free acid) and Salt and ester forms of compounds having HMG-CoA reductase inhibitory activity are included, and thus the use of such salts, esters, open acid and lactone forms is of interest.

  In some embodiments, in HMG-CoA reductase inhibitors in which an open acid form is present, the salt and ester forms are formed from such open acids, all such forms herein In the meaning of the term “HMG-CoA reductase inhibitor”. In some embodiments, the HMG-CoA reductase inhibitor is selected from lovastatin and simvastatin. In one embodiment, the HMG-CoA reductase inhibitor is simvastatin.

  As used herein, the term “pharmaceutically acceptable salt” with respect to an HMG-CoA reductase inhibitor means a non-toxic salt of the compound used, generally the free acid is converted to a suitable organic or inorganic salt. Produced by reacting with a base, in particular those formed from cations such as sodium, potassium, aluminum, calcium, lithium, magnesium, zinc, and tetramethylammonium, as well as ammonia, ethylenediamine, N- Methylglucamine, lysine, arginine, ornithine, choline, N, N′-dibenzylethiendiamine, chloroprocaine, diethanolamine, procaine, N-benzylphenethylamine, 1-p-chlorobenzyl-2-pyrrolidine-1′- Irmethylbenzimidazole, diethyla Emissions, piperazine, and tris salts formed from amines such as (hydroxymethyl) aminomethane. In other embodiments, additional examples of salt forms of HMG-CoA reductase inhibitors include acetate, benzenesulfonate, benzoate, bicarbonate, hydrogensulfate, hydrogen tartrate, borate, bromide. , Calcium hydroxyl, cansylate, carbonate, chloride, clavulanate, citrate, dihydrochloride, hydroxyl, edicylate, estrate, esylate, fumarate, glucoceptate, gluconate, glutamate, gluconyl Arsanilate, hexyl resorcinate, hydrabamine, hydrobromide, hydrochloride, hydroxynaphthoic acid, iodide, isothionate, lactate, lactobionate, laurate, malate, maleate, mandelic acid Salt, mesylate, methyl sulfate, mucato, napsylate, nitrate, Oleate, oxalate, pamoate, palmitate, pantothenate, phosphate / diphosphate, polygalacturonate, salicylate, stearate, subcetate, succinate, tannate , Tartrate, teolurate, tosylate, triethiodide, and valerate.

  In other embodiments, the ester derivatives of the described HMG-CoA reductase inhibitor compounds are cleaved to release the drug form when absorbed into the bloodstream of warm-blooded animals, resulting in improved therapeutic efficacy Acts as a pro-drag to give sex.

  Examples of HIV protease inhibitors include amprenavir, abacavir, CGP-73547, CGP-61755, DMP-450, indinavir, nelfinavir, tipranavir, ritonavir, saquinavir, ABT-378, AG1776, and BMS-232,632 It is done. Examples of reverse transcriptase include delaviridine, efavirenz, GS-840, HB Y097, lamivudine, nevirapine, AZT, 3TC, ddC, and ddI. HIV protease inhibitors such as indinavir or saquinavir have been reported to have potent anti-angiogenic activity and promote regression of Kaposi's sarcoma.

  “Angiogenesis inhibitors” refers to compounds that inhibit the formation of new blood vessels, regardless of mechanism. Examples of angiogenesis inhibitors include tyrosine kinase inhibitors such as inhibitors of tyrosine kinase receptors Flt-1 (VEGFRl) and Flk-1 / KDR (VEGFR20), epithelial cell-derived, fibroblast-derived or platelet-derived growth Inhibitors of factors, MMP (matrix metalloproteinase) inhibitors, integrin blockers, interferon-α, interleukin-12, polysulfate pentosan, cyclooxygenase inhibitors such as non-steroidal anti-inflammatory agents such as aspirin and ibuprofen ( NSAIDs), and selective cyclooxygenase-2 inhibitors such as celecoxib, valecoxib and rofecoxib, carboxamidotriazole, combretastatin A-4, squalamine, 6-O-chloroacetyl-cal Sulfonyl) - fumagillol, thalidomide, angiostatin, troponin-1, angiotensin II antagonists, and antibodies include for VEGF, but are not limited to.

  Other examples of angiogenesis inhibitors include endostatin, ukulein, lampyrinase, IM862, 5-methoxy-4- [2-methyl-3- (3-methyl-2-butenyl) oxiranyl] -1-oxaspiro [2, 5] Oct-6-yl (chloroacetyl) carbamate, acetyldinanaline, 5-amino-1-[[3,5-dichloro-4- (4-chlorobenzoyl) phenyl] methyl] -1H-1 , 2,3-triazole-4-carboxamide, CM101, squalamine, combretastatin, RPI4610, NX31838, sulfated mannopentose phosphate, 7,7- (carbonyl-bis [imino-N- Methyl-4,2-pyrrolocarbonylimino N-methyl-4,2-pyrrole] -carbonylimino] -bis- (1,3-naphthalenedisulfonate) and 3-[(2,4-dimethylpyrrol-5-yl) methylene] -2-indolinone ( SU5416), but is not limited to these.

  “Inhibitors of cell proliferation and survival signaling pathway” refer to pharmaceutical agents that inhibit cell surface receptors and signal transduction cascades downstream of those surface receptors. Such agents include inhibitors, inhibitors of EGFR (eg, gefitinib and erlotinib), inhibitors of ERB-2 (eg, trastuzumab), inhibitors of IGFR, inhibitors of CD20 (rituximab), cytokine receptors Inhibitors, inhibitors of MET, inhibitors of PDK (eg LY294002), serine / threonine kinases ((WO03 / 0886404, 03/0886403, 03/0886394, 03/088679, 02/083675, 02/0883139, 02/083140, and 02/083138), including but not limited to inhibitors of Raf kinase (for example, , BAY-43-9006), inhibitors of MEK (eg, I-1040 and PD-098059), and inhibitors of mTOR (for example, Wyeth CCI-779 and Ariad AP23573) can be mentioned. Such agents include small molecule inhibitor compounds and antibody antagonists.

  “Apoptosis-inducing agents” include, but are not limited to, activators of TNF receptor family members (including TRAIL receptors).

  “Agents that interfere with cell cycle checkpoints” refer to compounds that inhibit protein kinases that transmit cell cycle checkpoint signals, thereby sensitizing the cancer cell to DNA damaging agents. Such agents include inhibitors of ATR, ATM, Chkl and Chk2 kinases, and cdk and cdc kinase inhibitors, specifically 7-hydroxystaurosporine, flavopiridol, CYC202 (Cyccel) and BMS-387032. Illustrated.

  “Agents that interfere with receptor tyrosine kinases (RTKs)” refer to compounds that inhibit RTKs and thus inhibit mechanisms involved in tumor development and tumor progression. Such agents include, but are not limited to, tyrosine kinase inhibitors such as inhibitors of c-Kit, Eph, PDGF, Flt3 and c-Met. In addition, inhibitors of RTK are also included. Examples of “tyrosine kinase inhibitors” include N- (trifluoromethylphenyl) -5-methylisoxazole-4-carboxamide, 3-[(2,4-dimethylpyrrol-5-yl) methylidenyl) indoline-2- ON, 17- (allylamino) -17-demethoxygeldanamycin, 4- (3-chloro-4-fluorophenylamino) -7-methoxy-6- [3- (4-morpholinyl) propoxyl] -quinazoline, N- (3-ethynylphenyl) -6,7-bis (2-methoxyethoxy) -4-quinazolinamine, BIBX1382, 2,3,9,10,11,12-hexahydro-10- (hydroxymethyl) -10 -Hydroxy-9-methyl-9,12-epoxy-1H-diindolo [l, 2,3-fg: 3 ', 2', 1'-k ] Pyrrolo] [3,4-i] [1,6] benzodiazocin-1-one, SH268, genistein, ST1571, CEP2563, 4- (3-chlorophenylamino) -5,6-dimethyl-7-H- Pyrrolo [2,3-d] pyrimidinemethanesulfonate, 4- (3-bromo-4-hydroxyphenyl) amino-6,7-dimethoxyquinazoline, 4- (4′-hydroxyphenyl) amino-6,7-dimethoxyquinazoline , SU6668, SUl1248, STI571A, N-4-chlorophenyl-4- (4-pyridylmethyl) -1-phthalazine amine, and EMD12974.

  HDAC inhibitors are also useful in combination with platelet fibrinogen receptor (GP Iib / IIIa) antagonists such as tirofiban to inhibit cancer cell metastasis. Tumor cells are also highly activated by thrombin production. This activation is associated with the release of VEGF. The release of VEGF increases extravasation at the point of attachment to the vascular endothelium and enhances metastasis (Amirkhosravi, 1999, Plets 10: 285-292). Thus, in some embodiments, an HDAC inhibitor acts in combination with a GP Iib / IIIa) antagonist to inhibit metastasis. Examples of other fibrinogen receptor antagonists include abciximab, eptifibatide, cibrafiban, ramifiban, rotrafiban, chromofiban, and CT50352.

As used above, an “integrin blocker” is a compound that selectively antagonizes, inhibits or counteracts physiological ligand binding to α _v β ₃ integrin, selectively binds physiological ligand binding to α _v β ₅ integrin. A compound that antagonizes, inhibits, or counteracts, a compound that antagonizes, inhibits, or counteracts physiological ligand binding to both α _v β ₃ integrin and α _v β ₅ integrin, and certain integrins expressed on capillary endothelial cells A compound that antagonizes, inhibits, or counteracts the activity (including plural). The term also refers to antagonists of α _v β ₆ , α _v β ₈ , α ₁ β ₁ , α ₂ β ₁ , α ₅ β ₁ , α ₆ β ₁ , and α ₆ β ₄ integrins. The term also includes α _v β ₃ , α _v β ₅ , α _v β ₆ , α _v β ₈ , α ₁ β ₁ , α ₂ β ₁ , α ₅ β ₁ , α ₆ β ₁ , and α ₆ β _4. Also refers to any combination of integrins.

  Combinations with compounds other than anti-cancer compounds are also encompassed in the instant methods. For example, combinations of the claimed compounds of the present invention with PPAR-γ (ie, PPAR-gamma) agonists and PPAR-δ (ie, PPAR-delta) agonists are useful for the treatment of certain malignancies. PPAR-γ and PPAR-δ are nuclear peroxisome proliferator-activated receptors γ and δ. More recently, PPAR-γ agonists have been shown to inhibit the angiogenic response to VEGF in vitro, and both troglitazone and rosiglitazone maleate inhibit the development of retinal angiogenesis in mice. Examples of PPAR-γ agonists and PPAR-γ / α agonists include thiazolidinediones (eg, DRF2725, CS-011, troglitazone, rosiglitazone and pioglitazone), fenofibrate, bemfibrozil, clofibrate, GW2570, SB219994, AR-H039924. , JTT-501, MCC-555, GW2331, GW409544, NN2344, KRP297, NPOL10, DRF4158, NN622, GI262570, PNU182716, DRF552926, 2-[(5,7-dipropyl-3-trifluoromethyl-1,2- Benzisoxazol-6-yl) oxy] -2-methylpropionic acid (disclosed in US patent application Ser. No. 09 / 782,856), and 2 ( R) -7- (3- (2-Chloro-4- (4-fluorophenoxy) phenoxy) propoxy) -2-ethylchroman-2-carboxylic acid, but is not limited to these.

  In some embodiments, a compound having the structure of formula (A) or formula (I) is used in combination with gene therapy for the treatment of cancer. In other embodiments, gene therapy is used to deliver genes that suppress any tumor. Examples of such genes include p53 (which in some embodiments is delivered by recombinant virus-mediated gene transfer) Duc-4, NF-1, NF-2, RB, WT1, BRCA1, BRCA2. , UPA / uPAR antagonists, but not limited to.

  In other embodiments, the compound having the structure of Formula (A) or Formula (I) is combined with an inhibitor of inherent multidrug resistance (MDR), particularly MDR associated with high levels of expression of transport proteins. Is also administered. Such MDR inhibitors include inhibitors of p-glycoprotein (P-gp), for example, LY33579, XR9576, OC144-093, R101922, VX853 and PSC833 (Valspodar).

  In some embodiments, a compound having the structure of formula (A) or formula (I) is used to treat nausea or vomiting, including acute, delayed, late phase and preceding vomiting Used with antiemetics, which is accomplished by using a compound of formula (A) or formula (I) alone or in conjunction with radiation therapy. In a further embodiment, for the prevention or treatment of emesis, the compound of formula (A) or formula (I) may be replaced with other antiemetics, in particular a neurokinin-1 receptor antagonist, a 5HT3 receptor antagonist, eg ON Dansetron, granisetron, tropisetron and zasetetrone, GABAB receptor agonists such as baclofen, corticosteroids such as decadrone (dexamethasone), kenalog, aristocolt, nasalide, preferid, benecorten, or US Pat. No. 2,789,118 No. 2,990,401, 3,048,581, 3,126,375, 3,929,768, 3,996,359, 3,928,326 and Other as disclosed in 3,749,712 Of anti-dopaminergic drugs, for example, phenothiazines (eg, prochlorperazine, fluphenazine, thioridazine and mesoridazine), metoclopramide or used with dronabinol. In one embodiment, an anti-emetic agent selected from a neurokinin-1 receptor antagonist, a 5HT3 receptor antagonist and a corticosteroid is an adjunct for the treatment or prevention of emesis that occurs upon administration of a compound of the invention. Administer as an agent.

  In other embodiments, the compound having the structure of formula (A) or formula (I) is also administered with an agent useful for the treatment of anemia. Such an anemia treatment agent is, for example, a persistent erythrocytic receptor activator (eg, epoetin-α).

  In a further embodiment, the compound having the structure of formula (A) or formula (I) is also administered with an agent useful for the treatment of neutrophil depletion. Such a neutropenia therapeutic agent is a hematopoietic growth factor that controls the production and function of neutrophils such as human granulocyte colony stimulating factor (G-CSF). An example of G-CSF is filgrastim.

  In some embodiments, a compound having the structure of formula (A) or formula (I) is also administered with an immunopotentiator such as levamisole, bacilli Calmette Guerin, octreotide, isoprinosine and zadaxin.

  In other embodiments, the compound having the structure of Formula (A) or Formula (I) includes bone cancer in combination with bisphosphonates (understood to include bisphosphonates, diphosphonates, bisphosphonic acids and diphosphonic acids). It is also useful for the treatment or prevention of cancer. Examples of bisphosphonates include etidronate (Didronel), pamidronate (Aredia), alendronate (Fosamax), risedronate (Actonel), zoledronic acid (Zometa), iban Dronate (Boniva), incadronate or simadronate, clodronate, EB-1053, minodronate, neridronate, pyridronate, and tiludronate, and all pharmaceutically acceptable salts, derivatives, hydrates and mixtures thereof For example, but not limited to.

  In a further embodiment, compounds having the structure of formula (A) or formula (I) are also useful for the treatment or prevention of breast cancer in combination with an aromatase inhibitor. Examples of aromatase inhibitors include, but are not limited to, anastrozole, letrozole, and exemestane.

  In some embodiments, compounds having the structure of formula (A) or formula (1) are also useful for the treatment or prevention of cancer in combination with siRNA or RNAi treatment.

  In some other embodiments, compounds having the structure of formula (A) or formula (I) are also useful for the treatment or prevention of cancer in combination with compounds that induce terminal differentiation of neoplastic cells. Suitable differentiation agents include the following compounds: (A) polar compounds, (b) derivatives of vitamin D and retinoic acid, (c) steroid hormones, (d) growth factors, (e) proteases, (f) tumor promoters, and (g) inhibition of DNA or RNA synthesis. Agent.

  “DNA methyltransferase inhibitor” refers to a compound that inhibits the methylation of the DNA base cytosine at the C-5 position with DNA methyltransferase. Examples of such DNA methyltransferase inhibitors include DNA methyltransferase inhibitors, such as 5-azacytosine and zebralin®.

  Examples of antineoplastic agents are generally microtubule stabilizers (eg, paclitaxel (also known as Taxol®), docetaxel (Taxotere®), epothilone A, epothilone. B, also known as desoxyepothilone A, desoxyepothilone B or derivatives thereof), microtubule disruptors, alkylating agents, antimetabolites, epidophilotoxins, anti-neoplastic tumor enzymes, topoisomerase inhibitors, These include procarbazine, mitoxantrone, platinum coordination complexes, biological response modifiers and growth inhibitors, hormone / antihormonal therapeutics, and hematopoietic growth factors.

Examples of classes of antineoplastic agents include, for example, anthracycline family drugs, vinca drugs, mitomycin, bleomycin, cytotoxic nucleosides, taxanes, epothilone, discodermolide, pteridine family drugs, diynenes, and podophyllotoxins Is mentioned. Particularly useful members of this class include, for example, doxorubicin, carminomycin, daunorubicin, aminopterin, methotrexate, metopterin, dichloro-methotrexate, mitomycin C, porphyromycin, Herceptin®, Rituxan (Rituxan) (Registered trademark), 5-fluorouracil, 6-mercaptopurine, gemcitabine, cytosine arabinoside, colchicine, etoposide, etoposide phosphate or podophyllotoxin or podophyllotoxin derivatives such as teniposide, melphalan, vinblastine, vincristine, leurosidine , Vindesine, leulosin, paclitaxel and the like. Other useful antineoplastic agents include estracumtin, cisplatin, carboplatin, cyclophosphamide, bleomycin, tamoxifen, ifosamide, melphalan, hexamethylmelamine, thiotepa, cytarabine, idatrixate, trimethrexate, dacarbazine, L- Asparaginase, camptothecin, CPT-11, topotecan, ara-C, bicalutamide, flutamide, leuprolide, pyridobenzoindole derivatives, interferons, and interleukins. In some embodiments, the antineoplastic agent is a taxane and the antineoplastic agent is paclitaxel.
Radiation therapy

  Radiotherapy, also referred to as radiotherapy, is the treatment of cancer or other diseases with ionizing radiation. Ionizing radiation damages or destroys cells in the area being treated by damaging genetic material and making these cells unable to continue growing ("target tissue") Give energy. Radiation damages both cancer cells and normal cells, but the latter can repair itself and function properly. In some embodiments, radiation therapy is used to treat localized solid tumors such as skin, tongue, larynx, brain, breast, prostate, colon, uterus and / or cervical cancer. The In some embodiments, it is also used to treat leukemia and lymphoma (blood forming cells and lymphoid cancer, respectively).

  One type of radiation therapy commonly used involves photons, or “bundles” of energy. X-rays and gamma rays are both photon emissions used to treat cancer. The light rays are used to destroy cancer cells at the surface of the body or deeper in the body, depending on the amount of energy they have. In other embodiments, the higher the energy of the light, the deeper the target tissue will reach.

  Another approach to delivering radiation to cancer cells is to place the radioactive graft directly into the tumor or body cavity. This is called internal radiation therapy (brachytherapy, intratumoral and intracavitary radiation methods are types of internal radiation therapy). By using internal radiation therapy, the radiation dose is concentrated in a small area and the patient is only hospitalized for a few days. Internal radiation therapy is often used for cancer of the tongue, uterus, prostate, colon, and cervix.

  The term “radiotherapy” or “ionizing radiation” includes all forms of radiation, including α, β and γ radiation and ultraviolet radiation, and can directly or indirectly damage cellular or viral genetic material. The term “irradiation” refers to exposing the sample of interest to ionizing radiation. Radiation therapy with or without concurrent or subsequent chemotherapy is cancer of the head and neck, breasts, skin, anogenital organs, and certain non-malignant diseases such as keloids, desmoid tumors, hemangiomas, arteriovenous malformations and histiospheres This is an effective mode for proliferative disease X. However, the therapeutic effect is limited by radiation and chemotherapy-induced mucosal epithelial wounds and cutaneous radiation syndrome (CRS), including tissue swelling, mucositis, dermatitis, exfoliation and ulceration acute reactions, prolonged Examples include the development of effective tissue / dermatofibrosis, necrosis and sarcoma, squamous cell and defined cell carcinoma life-threatening sequelae.

  As used herein, at least one histone deacetylase inhibitor is used to cause at least one other therapeutic action, eg, normal tissue fibrosis induced by radiation or tissue necrosis induced by chemotherapy Methods for reducing side effects are provided, and also provided herein are methods for synergistic inhibition of tumor cell growth by radiation therapy and other anticancer agents.

  In a further aspect, a compound having the structure of formula (A) or formula (I) is administered in combination with a chemical agent that is believed to function by mimicking the effects of radiation therapy and / or by direct contact with DNA There is a way. In some embodiments, the agent used in combination with a compound of formula (A) or formula (I) to treat cancer includes cis-diamine dichloroplatinum (II) (cisplatin), doxorubicin, 5- Fluorouracil, taxol, and topoisomerase inhibitors include, but are not limited to, etoposide, teniposide, irinotecan and topotecan. Alkylating agents include, but are not limited to, BCNU, CCNU and MMS. Cross-linking agents include, but are not limited to, cisplatin and carboplatin.

  In some embodiments, the term “combination” exists as a fixed combination, a kit of parts, or an unfixed combination, as described below.

  A “fixed combination” is defined as a combination in which the first active ingredient and the second active ingredient are present together in one unit dosage form or in one. An example of a “fixed combination” is a pharmaceutical composition in which the first active ingredient and the second active ingredient are present in admixture for simultaneous administration, as in a single formulation. Another example of a “fixed combination” is a pharmaceutical combination in which the first active ingredient and the second active ingredient are present in one unit without being mixed.

  A “part kit” is defined as a combination in which the first active ingredient and the second active ingredient are present in a plurality of units. An example of a “part kit” is a combination in which the first active ingredient and the second active ingredient are present separately. In other embodiments, the components of the partial kits are administered separately, sequentially, simultaneously, in parallel, or staggered over time.

  In therapy, for example, (hyper) proliferation in response to the induction of certain diseases that are responsive or sensitive to inhibition of histone deacetylase, or apoptosis, such tumor formation or any of the cancer diseases described herein. At least one having the structure of formula (A) or formula (I) for use separately, sequentially, simultaneously, in parallel, or staggered over time in the treatment of sexually transmitted diseases and / or disorders A compound, at least one anti-cancer agent known in the art, eg, a second active ingredient that is one or more of the anti-cancer agents described hereinabove, and optionally a pharmaceutically acceptable carrier or diluent. Is provided.

Also,
(A) at least one compound having the structure of formula (A) or formula (I), formulated with a pharmaceutically acceptable carrier or diluent;
(B) at least one anticancer agent known in the art, such as, for example, an anticancer agent described hereinabove, formulated with a pharmaceutically acceptable carrier or diluent;
A recombinant product comprising is also provided.

  Also, at least one compound having the structure of formula (A) or formula (I) and medicament for use in therapy simultaneously, in parallel, sequentially, separately, or staggered over time Preparation of a pharmaceutically acceptable carrier or diluent and a second active ingredient that is an anticancer agent known in the art such as, for example, the anticancer agents described hereinabove and a pharmaceutically acceptable carrier or diluent. A partial kit comprising the preparation is also provided. In a further embodiment, the kit includes a disease that is responsive to or susceptible to histone deacetylase inhibition, eg, cell tumorigenesis, or a disease described herein that is different from cell tumorigenesis, particularly herein. Instructions for use in therapy to treat cancer, such as any of the cancer diseases described in.

  In some embodiments, the cancer treated by the methods provided herein includes: cardiac system: sarcoma (angiosarcoma, fibrosarcoma, rhabdomyosarcoma, liposarcoma), myxoma, rhabdomyosarcoma, fibrosis Tumor, lipoma, and teratoma, lung: bronchial cancer (squamous cell, undifferentiated small cell, undifferentiated large cell, adenocarcinoma), alveolar (bronchiole) cancer, bronchial adenocarcinoma, sarcoma, lymphoma, soft bone marrow Hamartoma, mesothelioma, gastrointestinal: esophagus (squamous cell carcinoma, adenocarcinoma, leiomyosarcoma, lymphoma), stomach (cancer, lymphoma, leiomyosarcoma), pancreas (tubular adenocarcinoma, islet cell tumor, glucagon-producing tumor) , Gastrin-producing tumor, carcinoid tumor, VIP-producing nematoma), small intestine (adenocarcinoma, lymphoma, carcinoid tumor, Kaposi's sarcoma, leiomyosarcoma, hemangioma, lipoma, neurofibroma, fibroma), large intestine (adenocarcinoma, Tubular gland type, chorionic gland type, hamartoma, leiomyoma), urine Organs: kidney (adenocarcinoma, Wilms tumor [nephroblastoma], lymphoma, leukemia), bladder and urethra (squamous cell carcinoma, transitional cell carcinoma, adenocarcinoma), prostate (adenocarcinoma, sarcoma), testicle (serum epithelium) Tumor, teratomas, embryonal carcinoma, teratocarcinoma, choriocarcinoma, sarcoma, stromal cell carcinoma, fibroma, fibroadenoma, adenomatous tumor, lipoma), liver: liver cancer (hepatocellular carcinoma), intrahepatic cholangiocarcinoma, Hepatoblastoma, hemangiosarcoma, hepatocellular adenocarcinoma, hemangioma, bone: osteosarcoma (osteosarcoma), fibrosarcoma, malignant fibrous histiocytoma, chondroma, Ewing sarcoma, malignant lymphoma (reticulosarcoma), multiple Myeloma, Malignant Giant Cell Tumor, Chordoma, Osteochron Flowoma (osteochondroostosis), Benign Chondroma, Chondroblastoma, Cartilage Myxofibromas, Osteoosteomas, and Giant Cell Tumor, Nervous System: Skull ( Osteoma, hemangioma, granuloma, xanthoma, osteoarthritis), meninges (meningiomas, meningosarcoma, glioma) Brain (astrocytoma, medulloblastoma, glioma, ependymoma, germinoma [pineoloma], pleomorphic glial blastoma, oligodendroma, schwannoma, retinoblastoma, congenital tumor ), Spinal cord (neurofibroma, meningioma, glioma, sarcoma), gynecology: uterus (endometrial cancer), cervix (cervical cancer, pre-tumor cervical dysplasia), ovary (ovarian cancer) [Serosa cystadenocarcinoma, mucinous cystadenocarcinoma, endometrioid tumor, abdominal blastoma (cellioblastoma), nominal cell carcinoma, unclassified cancer], granulosa-follicular membrane tumor, Sertoli-Leydig cell tumor, not yet Differentiated germinoma, malignant teratoma), vulva (squamous cell carcinoma, carcinoma in situ, adenocarcinoma, fibrosarcoma, melanoma), vagina (clear cell carcinoma, squamous cell carcinoma, saccular sarcoma [fetal rhabdomyosarcoma], Fallopian tube (carcinoma), hematology: blood (myeloid leukemia [acute and chronic], acute phosphorus Pablastic leukemia, chronic lymphocytic leukemia, myeloproliferative disease, multiple myeloma, myelodysplastic syndrome), Hodgkin disease, non-Hodgkin lymphoma [malignant lymphoma], skin: malignant melanoma, basal cell carcinoma, squamous cell carcinoma, Examples include, but are not limited to, Kaposi's sarcoma, dysplastic nevi, lipoma, hemangioma, dermal fibroma, keloid, psoriasis, and adrenal gland: neuroblastoma.

In some embodiments, acute myeloid leukemia (AML) and / or acute lymphocytic leukemia (ALL) is used in a monotherapy or combination therapy using a compound having the structure of formula (A) or formula (I). To treat. In addition to cancer, in some embodiments, a compound having the structure of formula (A) or formula (I) may be used in surgery, angioplasty, etc., such as autoimmune disease, arthritis, inflammatory bowel disease, etc. It is effective against a wide variety of hyperproliferative disorders, including but not limited to proliferation induced after medical practice including, but not limited to.
Antidiabetic

  In some embodiments, if the subject suffers from insulin deficiency (eg, type I diabetes), the subject is combined with a therapeutically effective amount of an HDAC inhibitor in combination with one or more other antidiabetic agents. (By the same or different routes of administration). Examples of anti-diabetic agents useful in combination with HDAC inhibitors include, but are not limited to, insulin secretagogues or insulin sensitizers, or other anti-diabetic agents. Examples of such antidiabetic agents include biguanides, sulfonylureas, glucosidase inhibitors, peroxisome proliferator activated receptor (PPAR) γ agonists such as thiazolidinedione, PPARα agonists such as fibrillic acid derivatives, P2 inhibitors, dipeptidyl Peptidase IV (DP4) inhibitors, sodium-glucose cotransporter type 2 (SGLT2) inhibitors, meglitinides, insulin and / or glucagon-like peptide-1 (GLP-I).

  In a further embodiment, the other antidiabetic agent is an oral antiglycemic agent, for example a biguanide such as metformin or phenformin or a salt thereof.

  In some other embodiments, the other antidiabetic agent is a sulfonylurea such as glyburide (also known as glibenclamide), glimepiride, glipizide, gliclazide or chlorpropamide, other known sulfonylureas, or pancreatic beta cell Other antiglycemic agents that act on ATP-dependent channels.

  In yet another embodiment, the antidiabetic agent is a glucosidase inhibitor, such as alkose or miglitol.

  In further embodiments, the HDAC inhibitor is troglitazone (Rezulin®), rosiglitazone, pioglitazone, MCC-555, GL-262570, englitazone (CP-68722) or darglitazone (CP-86325) , Isaglitazone, JTT-501, L-895645, R-119702, NN-2344 or YM-440 and used in combination with an insulin sensitizer.

  In other embodiments, the HDAC inhibitor is an antiglycemic agent such as insulin, or GLP-1 (1-36) amide, GLP-1 (1-36) amide, GLP-1 (7-37). Glucagon-like peptide-1 (GLP-1) and used in combination with AC2993 and LY-315902.

  In another embodiment, the other antidiabetic agent is PPAR. Such as AR-HO39242, GW-409544, KRP297. α / γ dual agonists, and by Murakami et al., "A Novel Insulin Sensitizer Acts As a Coligand for Peroxisome Proliferation - Activated Receptor α (PPARα) and PPARγ.Effect on PPARα Activation on Abnormal Lipid Metabolism in Liver of Zucker Fatty Rats", Diabetes 47, 1841-1847 (1998).

  In a further embodiment, the antidiabetic agent is a SGLT2 inhibitor.

  In yet a further embodiment, the antidiabetic agent is an αP2 inhibitor disclosed in US patent application Ser. No. 09 / 391,053 and provisional application 60 / 127,745, and has a dosage described herein. use.

In another embodiment, the antidiabetic agent is a DP4 inhibitor, such as provisional application 60 / 188,555, WO 99/38501, 99/46272, 99/67279 (PROBIODRUG), 99/67278 (PROBIODRUG), 99/61431 (PROBIODRUG), NVP-DPP728A (1-[[[2-[(5-cyanopyridin-2-yl) amino] ethyl] amino] Acetyl] -2-cyano- (S) -pyrrolidine), (tryptophyll-1,2,3,4-tetrahydro-isoquinoline-3-carboxylic acid, 2-cyanopyrrolidide, and 4-cyanopyrrolidide, described in the above references Use a dose of.
Growth hormone secretagogue

In another embodiment, the HDAC inhibitor is used in combination with one or more growth hormone secretagogues, such as arginine, L-3,4-dihydroxyphenylalanine (1-dopa), glucagon, vasopressin , PACAP (pituitary adenylyl cyclase active peptide), muscarinic receptor agonist, and synthetic hexapeptide, GHRP (growth hormone releasing peptide), but are not limited to these.
Other indications

  In further embodiments, HDAC inhibitors are used for diseases other than cancer, including systemic lupus erythematosus, rheumatoid arthritis, inflammatory diseases, and neurodegenerative diseases such as Huntington's disease.

In some embodiments, the methods and pharmaceutical compositions provided herein are used for the following indications:
(I) joint diseases and bone pathological diseases such as rheumatoid arthritis, osteoarthritis, ventilation, polyarthritis and psoriatic arthritis,
(Ii) autoimmune diseases such as systemic lupus erythematosus and graft rejection;
(Iii) hyperproliferative diseases such as smooth muscle cell proliferation including psoriasis or vascular proliferative disorders, atherosclerosis and restenosis,
(Iv) acute and chronic inflammatory and skin diseases such as ulcerative colitis, Crohn's disease, allergic rhinitis, allergic dermatitis, cystic fibrosis, chronic obstructive bronchitis and asthma,
(V) endometriosis, uterine fibroids, endometrial hyperplasia, and benign prostatic thickening;
(Vi) cardiac dysfunction,
(Vii) inhibition of immunosuppressive conditions such as HIV infection,
(Viii) in gene therapy, pathological conditions applicable to treatment by enhancing endogenous gene expression and enhancing transgene expression;
(Ix) Neuropathological disorders such as Parkinson's disease Alzheimer's disease or polyglutamine related disorders.

In general, neurodegenerative disorders treated by the methods provided herein are classified as follows.
I. Disorders characterized by progressive dementia in the absence of other prominent neurological signs, such as Alzheimer's disease, Alzheimer's type senile dementia, and Pick's disease (brain atrophy),
II. Syndromes of progressive dementia and other significant neurological abnormalities, such as
(A) Syndrome mainly appearing in adults (eg, Huntington's disease, dementia and ataxia and / or manifestation of Parkinson's disease combined, systemic atrophy, progressive supranuclear palsy (Steel Richardson Orzeowski) ), Diffuse Lewy body disease, and corticodentate substantia nigra degeneration), and (B) syndromes that primarily appear in children and young adults (eg, Hallerfolden-Spatz disease and progressive familial myoclonic epilepsy) ,
III. Abnormal syndromes with progressive posture and movement, such as tremor paralysis (Parkinson's disease), striatal nigra degeneration, progressive supranuclear paralysis, torsion dystonia (torsion spasm, deformed dystonia), Spastic torticollis and other movement disorders, familial tremor, and Jill Dou La Tourette syndrome,
IV. Syndrome of progressive ataxia, such as cerebellar degeneration (eg, cerebellar cortical degeneration and olive bridge cerebellar atrophy (OPCA)), and spinocerebellar degeneration (Friedreich ataxia and related disorders),
V. Central autonomic nervous system syndrome (Shy Dräger syndrome),
VI. Synergistic weakness and atrophy syndromes (motor neuropathies such as amyotrophic lateral sclerosis, spinal atrophy (eg infant spinal muscular atrophy (Welndich Hoffmann), juvenile spinal muscle) Atrophy (Wolfart Kugel Welander) and familial spinal muscular atrophy and other forms), primary lateral sclerosis, and hereditary spastic paraplegia,
VII. Syndromes that combine muscle loss and atrophy with sensory changes (progressive neuromuscular atrophy, chronic attributed polyneuritis), such as peroneus muscular atrophy (Charcot-Marie-Touse), hypertrophic interstitial pneumonia, ( De Juline Sotta), and various forms of chronic progressive neuropathy,
VIII. Syndrome of progressive blindness, such as retinitis pigmentosa (retinitis pigmentosa), and hereditary optic atrophy (Lever disease).

  In other embodiments, the methods and pharmaceutical compositions provided herein are also useful in smooth muscle cell proliferation and / or migration, and thus, for example, restenosis after angioplasty and / or stent implantation. It is useful for prevention and / or treatment.

The following preparations and examples are set forth in order to more clearly understand and to practice the methods and pharmaceutical compositions described herein. They should not be construed as limiting the scope of the description, but merely as illustrative and exemplary.
Biological Examples Example 1: Inhibition of HDAC

  Measurements are made in a 100 μL volume reaction using 96 well assay plates. In reaction buffer (50 mM HEPES, 100 mM KCl, 0.001% Tween-20, 5% DMSO, pH 7.4), HDAC-1 (200 pM final concentration) was mixed with inhibitors at various concentrations. And incubated for 30 minutes, after which trypsin and acetyl-Gly-Ala- (N-acetyl-Lys) -AMC are added at final concentrations of 50 nM and 25 μM, respectively, to initiate the reaction. As a negative control reaction, 8 replicates are performed in the absence of inhibitor.

  The reaction is monitored with a fluorescent plate reader. After a 30 minute lag time, the fluorescence intensity is measured in a 30 minute time frame using an excitation wavelength of 355 nm and a detection wavelength of 460 nm. The increase in fluorescence intensity over time is used as a measure of reaction rate. Inhibition constants are obtained using the BatchKi program (Kuzmic et al., 2000, Anal. Biochem. 286: 45-50).

Experiments have shown that trichostatin A, a hydroxamic acid histone deacetylase inhibitor, shows that histone acetylation increases with increasing drug dose. However, previous experiments provide evidence of increased histone acetylation after relatively low doses of HDAC inhibitors. For example, Buggy et al., 2006, Mol. Cancer Ther. , 5: 1309-17. The compounds described herein provide near-maximal histone acetylation at near-minimum doses of compound and duration of treatment.
Example 2: Inhibition of HDAC in cell extracts

HeLa nuclear extract (supplier: Biomol) is incubated with 2 × 10 ⁻⁸ M radiolabeled peptide substrate at 60 μg / ml. As a substrate for measuring HDAC activity, a synthetic peptide, ie, 14-21 amino acids of histone H4 is used. The NH ₂ -terminal part of the substrate is biotinylated with a 6-aminohexanoic acid spacer, the COOH-terminal part is protected with an amide group, and lysine 16 is specifically [ ³ H] acetylated. Substrate, biotin- (6-aminohexanoic acid) -Gly-Ala-([. Sup.3H] -acetyl-Lys-Arg-His-Arg-Lys-Val-NH.sub.2), 25 mM hepes Add 1M sucrose, 0.1 mg / ml BSA and 0.01% Triton X-100 to pH 7.4 buffer. After 30 minutes, the deacetylation reaction is stopped by adding HCl and acetic acid (final concentrations of 0.035 mM and 3.8 mM, respectively). After stopping the reaction, free ³ H-acetate is extracted with ethyl acetate. After mixing and centrifugation, the radiative formation of an aliquot of the upper (organic) phase is measured with a β-counter.

For each experiment, a control (containing HeLa nuclear extract and DMSO without compound), a blank culture (containing DMSO but no HeLa nuclear extract or compound), and a sample (compound dissolved in DMSO and HeLa) (Including nuclear extract) to equilibrate. Initially, compounds are tested at a concentration of 10 ⁻⁵ M. If the compound shows activity at 10 ⁻⁵ M, a concentration response curve is generated that tests the compound at a concentration between 10 ⁻⁵ M and 10 ⁻¹² M. In each test, the blank value is subtracted from both the control value and the sample value. The control sample shows 100% substrate deacetylation. For each sample, radioactivity is expressed as a percentage of the average value of the control. Where appropriate, IC ₅₀ values (concentration of drug required to reduce the amount of metabolite to 50% of control) are calculated using probit analysis of stepwise data. In some embodiments, the effect of the test compound is expressed as pIC ₅₀ (negative log value of the IC ₅₀ value).
Example 3: In vitro cell proliferation assay

  The ability of compounds of formula (A) or formula (I) to inhibit tumor cell growth in vitro was determined as follows.

Stock cultures of HCT116 colon cancer and other cell lines were cultured at 37 ° C. in a 5% CO ₂ humidity atmosphere with 10% (v / v) fetal calf serum, 2 mM L-glutamine, 1 mM sodium pyruvate, Maintain in RPMI medium 1640 containing 50 units / ml penicillin and 50 μg / ml streptomycin. Cells are cultured in 75 cm ² culture flasks and subcultures are made every 3-4 days so that the cells do not confluent more than 90%.

  For proliferation assays, HCT116 cells were harvested by trypsin treatment (0.05% trypsin / 0.53 mM EDTA), washed twice in culture, resuspended in an appropriate volume of culture, and then Count using a hemocytometer. Cells are seeded in flat bottom 96 well plates at a density of 5,000 cells / well in 100 μl. Cells are allowed to bind for 1.5 to 2 hours at 37 ° C.

Compounds are diluted in 10 mM mother liquor in DMSO. Three-fold serial dilutions are performed in culture medium containing 0.6% DMSO in wells (3 wells) of a 96-well U-bottom plate, starting with a 60 μM solution. After dilution is complete, 100 μl of each compound dilution (3 wells) is transferred to designated wells of a 96 well plate containing cells in 100 μl of culture medium. The final concentration of the dose response for the compound in the assay plate is in the range of 0.12-30 μM. Control wells (untreated cells) receive 100 μl of 0.6% DMSO in culture. Wells containing cell-free culture medium serve as background wells. Cells are cultured with compounds for 48 and 72 hours at 37 ° C. in a humidified CO ₂ incubator.

Cell proliferation is assessed by measuring fluorescence intensity after adding a fluorescent redox indicator, Almar Blue ™ (BioSource International). 10 μl Alamar Blue ™ is added to each well of the 96 well plate (s) 3-4 hours prior to the end of the incubation time. Take assay plate values with a fluorescent plate reader (excitation: 530 nM, emission: 620 nM). Compound GI ₅₀ values (concentration at which tumor cell growth is inhibited by 50%) are determined by plotting the percent of control fluorescence intensity against the log of compound concentration.
Example 4: Determination of antiproliferative activity on A2780 cells

Human A2780 ovarian cancer cells are cultured in RPMI 1640 culture medium supplemented with 2 mM L-glutamine, 50 μg / ml gentamicin and 10% fetal calf serum. Cells are always maintained as monolayer cultures at 37 ° C. in a humidified 5% CO ₂ atmosphere. Cells are passed once a week using a trypsin / EDTA solution at a split ratio of 1:40. All culture media and additives are obtained from Life Technologies. Cells were not contaminated with mycoplasma as determined using the Gen-probe mycoplasma tissue culture kit (BioMrieux).

Cells are seeded in NUNC ™ 96-well culture plates (Life Technologies) and allowed to adhere to plastic overnight. The density used for plating is 1500 cells / well in a culture medium with a total volume of 200 μl. After cell attachment to the plate, the culture medium is changed and drugs and / or solvents are added to a final volume of 200 μl. After 4 days of culture, the medium is replaced with 200 μl of fresh medium and cell density and viability are assessed using an MTT-based assay. To each well, 25 μl of MTT solution is added and the cells are further incubated at 37 ° C. for 2 hours. The medium is then carefully aspirated and the blue MTT formazan product is solubilized by adding 25 μl glycine buffer followed by 100 μl DMSO. The micro test plate is shaken for 10 minutes on a microplate shaker and the absorbance at 540 nm is measured using an Emax 96 well spectrophotometer (Sopachem). In the experiment, the result of each experimental condition is the average of 3 replicate wells. For initial screening purposes, compounds are tested at a single fixed concentration of 10 ⁻⁶ M. The experiment is repeated for the active compound until a complete concentration response curve is obtained.

For each experiment, controls (no drug) and blank cultures (no cells or drugs) are run in parallel. The blank value is subtracted from all control and sample values. For each sample, the average value of cell growth (in absorbance units) is expressed as a percentage of the average value of control cell growth. Where appropriate, IC ₅₀ values (concentration of drug required to reduce cell growth to 50% of control) are calculated using probit analysis of stepwise data (Finney, DJ, Probit). Analyzes, 2nd edition, Chapter 10, Graded Responses, Cambridge University Press, Cambridge 1962). The effect of the test compound is expressed as pIC ₅₀ (negative log value of IC ₅₀ value).
Example 5: Mechanism of sensitivity of primary hematopoietic tumors and tumor cell lines to HDAC inhibitors

  Test that a test compound having the structure of formula (A) or formula (I) inhibits growth and induces apoptosis in various hematopoietic cell lines derived from B-, T- and myeloid malignancies did. Growth inhibition and apoptosis were described at drug concentrations of ≦ 0.125 μM and were accompanied by known biochemical markers of HDAC inhibition including histones and tubulin hyperacetylation. Consistent with these results, Olive et al. Found that HDAC inhibitors were used in exponentially growing SiHa cervix and WiDr colon cancer cells in a relatively narrow drug concentration range resulting in maximum growth inhibition. I found out that These results are in contrast to other hydroxamates such as suberoylanilide hydroxamic acid (SAHA), which are dose dependent. Olive et al., 2007, Clin. Cancer Res. 13 (22). The test compound was also active in an animal xenograft model of hematopoietic disease. The test compound has a good pharmacokinetic and pharmacodynamic profile in animal models and humans. To demonstrate the potential clinical utility of test compounds in hematopoietic tumors, primary leukemia samples were isolated from patients and screened for resistance to test compounds in vitro. Of these 19 primary samples (10 acute myeloid leukemias (AML) and 9 acute lymphoblastic leukemias (ALL)), some were derived from patients who failed standard treatment None of them were resistant to the test compound at 0.5 uM, and only 2 (1 AML and 1 ALL) were considered resistant at 50 nM. Gene expression analysis using DNA microarrays from these primary tumors revealed changes in gene expression consistent with HDAC inhibition and defined a potential pathway for the activity of this compound in these tumors. Some of these pathways have been analyzed biochemically, and as a result there is much commonality, but it has been shown that different mechanisms of induction of apoptosis can work in different cell lines and primary tumors. It was done.

These results demonstrate that the test compound is very active in vitro in cell lines derived from hematopoietic tumors and is a preclinical model in vivo. Furthermore, the high sensitivity of primary leukemia tumors to treatment with in vitro test compounds in combination with the predicted pharmacokinetics in humans, in some embodiments, patients with hematopoietic malignancies, particularly AML and ALL Suggests that it may be highly responsive to treatment with HDAC inhibitors in the clinic.
Example 6: Inhibition of homologous recombination and disruption of RAD51 foci by HDAC inhibitors

  In order to investigate the specific effect in double-strand break repair (DSBR) of test compounds having the structure of formula (A) or formula (I), modified due to either genetic alterations or small molecule inhibitors Cell lines with a DNA repair pathway were evaluated. Proteins important in CHO cells lacking Ku86 (xrs5), non-homologous end joining (NHEJ) were analyzed by clonal protozoal survival after treatment with various doses of test compound. The xrs5 cell line showed an 8-fold reduction in clonal protozoa production when compared to the parental CHO-K1 cell line. In contrast, cell lines lacking homologous recombination (HR), such as BRCA1 mutant cells, did not show such differences. The use of 1,5-isoquinolinediol (IQD), which inactivates the basic excision repair protein poly-ADP ribose polymerase (PARP), creates lesions that are thought to be repaired by HR. IQD given to Ramos cells in combination with test compounds produced a synergistic effect on cell death as measured by Annexin V / propidium iodide positive cells. At the same time, these results suggest that the test compound acts by specifically inhibiting HR. These results indicate that the histone deacetylase inhibitors described herein do not appear to affect non-homologous end joining, as evidenced by no change in the initial rate of repair movement. This is consistent with the work of Olive et al.

  To explore this feature, the levels of essential proteins in RAD51, HR were analyzed by Western blotting and immunofluorescence. After HCT116 cells were exposed to doses of test compound ranging from 0.2 μM to 2.0 μM, RAD51 levels decreased to 20% of controls by 24 hours, but remained unchanged at 6 hours. Real-time PCR analysis demonstrated that RAD51 transcription levels were also decreased in both HCT116 and DLD-1 cells. Finally, RAD51 nuclear foci were visualized after γ-irradiation. Pretreatment with 0.2 μM test compound resulted in complete inhibition of RAD51 foci formation and complete removal of RAD51 from the nucleus.

These observations suggest that test compounds inhibit HR by down-regulating RAD51 gene expression and affecting the ability of cells to form RAD51 foci at the lesion site. These observations are that in some embodiments of formula (A) or formula (I) used in combination with therapeutic agents that produce lesions repaired by HR, such as γ-irradiation, cisplatin and oxaliplatin. Compounds with structure indicate that it is beneficial to use RAD51 as a biomarker to predict clinical efficiency.
Example 7: Biomarker related to antiproliferative effect of HDAC inhibitor

  The antiproliferative effect of the compound of formula (A) or formula (I) on HCT116 cell proliferation is analyzed in an Alamar Blue ™ fluorometric assay as described by deFries and Mitsuhashi (1995). Briefly, HCT116 cells (5000 cells / well in 100 μl) were cultured in complete medium (10% (v / v) fetal calf serum, 2 mM L-glutamine, 1 mM sodium pyruvate in RPMI in a 96 well plate. Plate in culture medium 1640). Test compounds are diluted in 20 mM mother liquor with DMSO. Serial dilutions are started in a culture medium containing 0.6% DMSO in wells (3 wells) of a 96-well U-bottom plate, starting with a 60 μM solution. After dilution is complete, 100 μL of test compound dilution (3 parts) is transferred to the designated wells of a 96-well plate containing cells in 100 μl culture medium. Control wells (untreated cells) receive 100 μl of 0.6% DMSO in culture. The final DMSO concentration in each well was 0.3%. Wells containing cell-free culture medium serve as background wells. Cells are cultured with compounds for 48 hours.

Cell proliferation is assessed by measuring fluorescence intensity after adding a fluorescent redox indicator, Almar Blue ™ (BioSource International). 10 μl Alamar Blue ™ is added to each well of the 96-well plate (s) 4 hours prior to the end of the incubation period. Take assay plate values with a fluorescent plate reader (excitation: 530 nM, emission: 620 nM). GI ₅₀ values (concentration at which tumor cell growth is inhibited by 50%) are determined by plotting the percent of control fluorescence intensity against the log of test compound concentration.

Next, the exposure time required to reach GI ₅₀ is determined. Briefly, HCT116 cells were plated into 96-well plates as described in the proliferation assay and intermittently used with test compounds (0.3% final DMSO concentration) for various lengths of time. Dosage, wash, then analyze in drug-free medium for 48 hours and calculate GI ₅₀ values.

  To understand the biochemical events associated with the anti-proliferative effects of test compounds, the cellular levels of acetylated tubulin, phospho-H2AX, and cytokeratin 18 fragment aa387-397 are determined. Importantly, acetylated tubulin is a marker for HDAC inhibition, whereas phospho-H2AX and cytokeratin 18 fragment aa387-397 are early markers of apoptosis.

For this purpose, HCT116 cells are cultured in 24-well plates for various lengths of time (ie 5 minutes, 15 minutes, 1 hour, 2 hours, 6 hours, 12 hours and 18 hours), test compound concentrations. Are administered intermittently (0.01 μM, 0.1 μM, 0.5 μM, 5 μM and 10 μM, final DMSO concentration of 0.2%). After treatment, cells are collected and lysed in M-Per lysis buffer (Pierce) containing protease and phosphatase inhibitors according to the manufacturer's instructions. Lysate (20 ug total protein) is solubilized in SDS-PAGE reducing sample buffer, boiled and electrophoresed in a 16% Tris-Glycine gel (Invitrogen). The gel was then blotted onto nicocellulose (22um membrane, Invicogen) and monoclonal anti-acetylated tubulin antibody (clone 6-11-1, Sigma) or polyclonal anti-phospho-H2AX antibody (catalog number: 2577, (Phosphohistone H2AX, Ser139 antibody, Cell Signaling). Blots examined with anti-acetylated tubulin antibody were then cultured with anti-mouse peroxidase-conjugated secondary antibody (Pierce), and enhanced chemiluminescent blots using SuperSignal West Femto Maximum Sensitivity substrate (Pierce). And deploy according to the manufacturer's instructions. The blot examined with the anti-phospho-H2AX antibody was then cultured with a peroxidase-conjugated anti-rabbit secondary antibody and the enhanced chemiluminescent blot was used with the SuperSignal West Pico Kit (Pierce). Deploy according to the letter. Detection of cytokeratin 18 fragment aa 387-397 uses the M30 Apoptosense ELISA kit (distributed by Peviva, Sweden, Alexis Biochemcals) and cell lysates (5 figure total protein) are evaluated according to the manufacturer's instructions.
Example 8: Early biomarkers associated with anti-tumor response of HDAC inhibitors

  To understand early biochemical events associated with the antiproliferative effects of test compounds having the structure of formula (A) or formula (I), the cellular level of phospho-H2AX is determined. Importantly, phospho-H2AX is an early marker of apoptosis. After the test compound is administered to HCT116 cells and HeLaS3 cells, accumulation of γ-H2AX, which is an early indicator of antitumor response, is measured.

To better understand the accumulation of γ-H2AX at earlier time points, two cell lines, HCT-116 and HeLaS3, were treated with HDAC inhibitory test compounds and γ-H2AX was treated with Western blot and cellular immunity. Monitor with both fluorescence methods. Both HCT-116 cells and HeLaS3 cells were either complete cultures in 24-well dishes or 4-well chamber slides (containing McCoy for HCT116, 10% FBS and 1XPen / Strep, and 1: 1 mix of DME / HamFl2 for HeLaS3, 10 % FBS, 2 mM L glutamine and 1 XPen / Skep) overnight (18 hours) and treated with test compound from 1 mM mother liquor in DMSO to give a final concentration of 0, 0.1 1, 3 or 10 μM. Cells are grown with compounds for 1 or 2 hours of growth, at which point the media is removed and the cells are washed once with phosphate buffered saline (PBS). For Western blot analysis and lysis, lysates from heated and untreated cells (20 μg total protein) were electrophoresed and blotted onto PVDF, which was diluted 1: 1000 with polyclonal anti-phospho- Check with H2AX antibody (purchased from Cell Signaling). The blot is then doubled at a dilution of 1: 10,000 using a secondary antibody coupled with anti-rabbit IgG HRP and developed with enhanced chemiluminescence detection. For cellular immunofluorescence staining, treated cells are washed once with PBS, fixed and permeabilized cells are stained with a monoclonal anti-phospho-H2AX antibody (from Upstate) at a dilution of 1: 500. The slides are then cultured 1: 2000 with anti-mouse IgG AF488 (from Molecular Probes) and mounted on Profound Gold antifade using DAPI for immunofluorescence imaging.
Example 9: Immunofluorescence staining of human cells

Monolayer cultures of different cells are grown in Dulbecco's MEM broth supplemented with 10% fetal bovine serum and antibiotics. Cells are detached from the culture flask by gentle trypsinization, pelleted, and phosphate buffered saline (PBS, 136 mM NaCl, 2 mM KCl, 10.6 mM NaHPO ₄ , 1.5 mM KH ₂ PO ₄ [ pH 7.3]) and pre-warmed at 37 ° C. (Haaf et al., 1995, Proc. Natl. Acad. Sci USA 92: 2298-2302). The cultured cells are washed and resuspended in PBS. The density of the somatic cells in PBS, adjusted to 10 ⁵ cells / ml. An aliquot (0.5 ml) of the cell suspension is centrifuged on a clean glass slide using Cytospin (Shandon, Pittsburg) at 800 rpm for 4 minutes. Immediately after centrifugation of the cells, the slide is fixed in methanol at -20 ° C. for 30 minutes and then immersed in ice-cold acetone for a few seconds to permeabilize the cells for antibody staining. After washing three times with PBS, the specimens were used in a humidified incubator with rabbit anti-HsRad51 antiserum diluted 1:50 with PBS containing 0.5% bovine serum albumin at 37 ° C. for 30 minutes. Incubate. Slides are washed 3 times for 10 minutes each and then incubated with fluorescein-isothiocyanate (FITC) conjugated anti-rabbit IgG diluted 1:20 in PBS for 30 minutes. After three washes with PBS, the specimens were counterstained with 4 ′, 6-diamidino-2-phenylindole (DAPI, 0.1 ug / ml, 1 minute) and antifade {90% (volume / volume) glycerol. /0.1m Tris-HCl, pH 8.0) /2.3% l, 4-diazabicyclo [2.2.2] octane (DABCO)}.

Images are taken with a thermoelectrically cooled charge coupled device (CCD) camera (PM512 model, Photometries, Tucson, Ariz.) Controlled by an Apple Macintosh computer using a Zeiss epifluorescence microscope. The grayscale source image is captured separately with a filter set for fluorescein and DAPI. Grayscale source images are pseudo-stained and synthesized using Oncor Image and Adobe Photoshop software. Using a CCD imaging system, all antibody signals were clearly visible to the naked eye through a microscope. Immunostaining of different cell lines shows that HsRad51 is enriched at small isolated sites (lesions) throughout the nucleus and largely excluded from the nucleus and cytoplasm.
Example 10: Detection of RAD51 expression level protein by Western blotting

For determination of protein levels by Western blotting, cell extracts are prepared as follows. Cells are scraped and collected, washed with PBS and pelleted by centrifugation. The cell pellet (from a 100 mm plate) is resuspended in 200 μl B3 buffer containing protease inhibitors, shaken at 4 ° C. for 10 minutes, and centrifuged at 12,000 rpm for 10 minutes at 4 ° C. using a Tomy microcentrifuge. To do. To make 1 l of B3 buffer, 1 ml NP-40, 50 ml 5 M NaCl, 10 ml 0.5 ml EDTA, 50 ml 1 M Tris HCl are added at pH 7.5 to 889 ml dH ₂ O. On the day of cell harvest, protease inhibitors are added to B3 buffer (aprotinin, leupeptin and pepstatin to final concentrations of 2 μg / ml, 5 μg / ml and 0.7 μg / ml, respectively). The supernatant is saved for Western blot analysis. Sample protein concentration is determined by Bradford assay (BioRad, Richmond, Calif.). Typically, 50 μg of protein is separated by electrophoresis on a 10% SDS-polyacrylamide minigel (Mini Protean II, BioRad, Richmond, Calif.) At 120 V, 150 mA for 1.5 hours. Proteins were transferred to nitrocellulose (Protran nitrocellulose, Schleicher and Schuell, Schuell, Schuell, Schuell, Schuell, Schuell and Schuell, Schuell and Schuell, Schuell and Schuell, Schuell and Schuell, Schuell and Schuell, Schuell, Schuell, and Schueller. ). Nitrocellulose filter blocking is performed overnight at 4 ° C. in 5% milk in PBS / 0.2% Triton X-100. The minimum blocking time is 10 minutes. Discard the liquid and add 5 ml of anti-RAD51 polyclonal antibody (Dilute Oncogene Research Products, Ab1, Calbiochem, Cambridge, Mass., 1: 500).

The nitrocellulose membrane was shaken for 1 hour at room temperature, washed 3 times for 5 minutes in Tris-buffered saline (TBS) containing 0.2% Triton X-100, and again 0.2% Tris X-100. Block with 5% milk in TBS containing for 10 minutes. Secondary antibody (goat anti-rabbit for anti-RAD51 antibody, 1: 1000) is added to fresh TBS containing 0.2% Triton x-100 and milk, shaken for 20-40 minutes, and 0.2% Triton X- Three 10 minute washes with TBS containing 100 are performed. Western blots are developed using Super Single (Pierce, Rockford, Ill.) According to the kit protocol. Kodak X-OMAT AR film is exposed for 10 seconds to 1 minute.
Additional methods

  Western blot analysis: Cell lines [all NHL except Jurkat (T cell leukemia) and K562 (CML)] were treated with PCI-24781 for a given time, lysed, total protein quantified, Western blot Analysis was performed. RAD51 and actin antibodies were obtained from Santa Cruz.

  Taqman gene expression assay: Ten lymphoma cell lines were treated with PCI-24781 for various times, and total RNA was isolated and quantified. The Tacman assay was set up using Tacman Master Mix (Applied Biosystems) and 50 ng of total RNA as a template. A gene expression assay test set for RAD51 was purchased from Applied Biosystems.

  Annexin V staining: Annexin-V after 96 hours of treatment with a specific dose of drug alone or in combination to determine potential synergy between PCI-24781 and PARP inhibitor PJ34 in HCT116 cells Staining was used to assess cytotoxicity. The Calcusyn program (Biosoft) was used to create a combination index that determined whether there was synergy, additive or antagonism between the two drugs.

Tissue microarray in primary tumors: First diagnostic fixed and paraffin-embedded histological tissues of FL and DLBCL samples obtained from the Northwestern University Pathology Archive were used with the approval of IRB to create a TMA. Slides containing 5 micron sections were stained with mouse anti-Rad51 mAB (# NA71, Calbiochem, San Diego, Calif.) And processed with the DakoCytomation EnVision + system (Dako Corporation, Carpinteria, Calif.), And ACIS II computerized. Used and scored by pathologist.
Example 11: Baseline RAD51 expression in lymphoma

Non-Hodgkin lymphoma (NHL) cell lines were tested (see FIG. 3) and all cell lines expressed RAD51 protein by Western blotting with the lowest levels in HH, cutaneous T-cell lymphoma cell lines .
Example 12: 3-((Dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide inhibition and sensitization of DNA repair by homologous recombination

3-((Dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide inhibited DNA repair by homologous recombination, as shown in FIG. Cells were sensitized to radiation and DNA-damaging agents by down-regulating RAD51. FIG. 2 shows RAD51 up to 24 hours at the mRNA (left) and protein (right) levels in the HCT-116 colon tumor cell line in vitro and in vivo (not shown). Of irradiated HCT-116 cells even when pretreated with 3-((dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide for 24 hours. The RAD51 foci in the nucleus were completely disappeared (not shown, see Adimoool et al., 2007, PNAS epub, 27 November, which is incorporated herein by reference).
Example 13: RAD51 tissue microarray

The tissue microarray represented in FIG. 4 shows RAD51 overexpression in multiple primary lymphoma tumors. RAD51 expression of immunohistochemical staining in human DLBCL tumor samples from a tissue microarray (TMA) containing 229 primary tumor parts (138 follicular lymphomas and 91 DLBCL). 78% of samples of each tumor type in TMA expressed mid to high levels of RAD51.
Example 14: Downregulation of RAD51 protein in lymphoma cell lines

When non-Hodgkin cell lines were treated with 3-((dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide for most cell lines tested In a dose-dependent manner, down-regulation of RAD51 protein levels was shown. The HH cell line showed minimal effect (see Figure 5).
Example 15: RAD5l transcription downregulation by quantitative RT-PCR

The cell line was treated with 3-((dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide for 24 hours and RAD51 mRNA was analyzed by Taqman RT-PCR. analyzed. According to Western blotting and analysis, 3-((dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide is more than doubled in most cell lines , It was found that there was down-regulated RAD51 mRNA expression (see FIG. 6), and the HH cell line did not show a decrease in RAD51.
Example 16: 3-((Dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide-induced apoptosis

After 48 hours of culture, 3-((dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide-induced apoptosis in lymphoma cell lines was analyzed by Annexin V-FITC flow. Measured by cytometry. A dose-dependent increase in apoptotic cell death was observed in all cell lines except the HH lymphoma cell line, and lower levels of apoptosis were also observed in all cell lines at 24 hours (see FIG. 7). . The level of RAD51 expression was reduced, each of the five cell lines showed> 70% apoptosis, and> 4 fold reduction in RAD51 mRNA after drug treatment. Conversely, HH cell lines with minimal% apoptosis had the lowest pretreatment level of RAD51, as well as the lowest reduction in treatment. Thus, both the initial level of RAD51 in the tumor and the multiple of the post-treatment decrease is 3-((dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide activity Can be predicted and in some embodiments is most likely to react with 3-((dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide. This is used as a biomarker in clinical studies to identify high patients.
Example 17: Correlation of RAD51-expressing biomarker with apoptosis

Different correlations between 3-((dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide-induced down regulation of RAD51 and% apoptosis Measured by the method. FIG. 8A shows baseline RAD51 expression levels by Western blot. RAD51 protein reduction was measured in cells treated with 3-{(dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide (see FIG. 8B). After treatment with 3-((dimethylamino) methyl) -N- (2- {4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide, reduction of RAD51 protein and mRNA correlates with% apoptosis Was determined (see FIG. 8C). Furthermore, a correlation between mRNA expression and% apoptosis was also found, as shown in the correlation plot of FIG. 8D.
Example 18: Treatment of HDAC inhibitors and doxorubicin

  The combination of 3-{(dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ethyl) benzofuran-2-carboxamide and doxorubicin administered simultaneously is a non-Hodgkin cell line, DHL-4 and In DLCL2, it showed a synergistic effect, but less than in HH cell lines, where RAD51 levels were low and 3-((dimethylamino) methyl) -N- (2- (4- (hydroxycarbamoyl) phenoxy) ) Ethyl) not reduced by benzofuran-2-carboxamide.

  Numerous embodiments are described throughout the specification, claims and accompanying drawings. However, in some embodiments, various modifications may be made without departing from the spirit and scope of the description. Accordingly, other embodiments are within the scope of the following claims.

Claims (25)

A method of treating a disease, disorder or condition associated with a deficiency in non-homologous end joining of DNA comprising:
(A) inhibits the activity of at least one therapeutically effective amount of RAD51 in a patient suffering from a disease, disorder or condition associated with a deficiency in non-homologous end joining of DNA, or prevents the formation of RAD51 foci, or Administering an agent that prevents the construction of a functional repair complex for homologous recombination of DNA;
(B) administering to the patient a treatment capable of damaging cellular DNA;
Including methods.   The at least one agent that inhibits the activity of RAD51, prevents the formation of RAD51 foci, or prevents the construction of a functional repair complex for homologous recombination of DNA is a therapeutically effective histone deacetylase. The method of claim 1, wherein the method is a ase inhibitor, or a pharmaceutically acceptable derivative thereof.   2. The method of claim 1, wherein the defect in non-homologous end joining of DNA comprises a defect in a gene selected from the group consisting of Ku70, Ku80, Ku86, Ku, PRKDC, LIG4, XRCC4, DCLRE1C and XLF.   The disease, disorder or condition is breast cancer, colon cancer, colorectal cancer, non-small cell lung cancer, small cell lung cancer, liver cancer, ovarian cancer, prostate cancer, cervical cancer, bladder cancer, gastric cancer, gastrointestinal stromal tumor, Pancreatic cancer, germ cell tumor, mast cell tumor, neuroblastoma, mastocytosis, testicular cancer, glioblastoma, astrocytoma, lymphoma, melanoma, myeloma, acute myeloid leukemia (AML), acute The method of claim 1, wherein the cancer is selected from lymphoid leukemia (ALL), myelodysplastic syndrome, chronic myelogenous leukemia, Burkitt lymphoma, chronic myelogenous leukemia, and B-cell lymphoma.   The method of claim 1, wherein the treatment capable of damaging cellular DNA is administered when the expression level of RAD51 is within a predetermined range.   3. The method of claim 2, wherein the therapeutically effective amount of the at least one histone deacetylase inhibitor is from about 0.2 mg to about 2000 mg. Said at least one histone deacetylase inhibitor is of formula (I):
(Where
R ¹ is hydrogen or alkyl;
X is —O—, —NR ² —, or —S (O) _n, where n is 0-2 and R ² is hydrogen or alkyl;
Y is alkylene optionally substituted with cycloalkyl, optionally substituted phenyl, alkylthio, alkylsulfinyl, alkylsulfonyl, optionally substituted phenylalkylthio, optionally substituted phenylalkylsulfonyl, hydroxy, or optionally Substituted phenoxy,
Ar ¹ is phenylene or heteroarylene, wherein said Ar ¹ is optionally substituted with one or two groups independently selected from alkyl, halo, hydroxy, alkoxy, haloalkoxy or haloalkyl And
R ³ is hydrogen, alkyl, hydroxyalkyl, or optionally substituted phenyl;
Ar ² is aryl, aralkyl, aralkenyl, heteroaryl, heteroaralkyl, heteroaralkenyl, cycloalkyl, cycloalkylalkyl, heterocycloalkyl, or heterocycloalkylalkyl. )
And a single stereoisomer, single geometric isomer, or a mixture thereof, or a pharmaceutically acceptable salt thereof.   6. The method of claim 5, wherein the predetermined range of RAD51 expression levels is less than about 70% compared to the RAD51 expression level prior to the administration of the at least one histone deacetylase inhibitor. .   Said treatment capable of damaging cellular DNA comprises radiation therapy, or administration of a pharmaceutically effective amount of at least one anticancer agent, known combination schemes for cancer treatment, or any combination thereof, The method of claim 1.   The method of claim 9, wherein the treatment capable of damaging cellular DNA is radiation therapy.   The anticancer agent is a cytotoxic agent / cytostatic agent, antiproliferative agent, prenylprotein transferase inhibitor, HMG-CoA reductase inhibitor, nitrogen mustard, nitrosourea, angiogenesis inhibitor, cell proliferation and survival signal 10. The method of claim 9, wherein the method is a pathway inhibitor, an apoptosis-inducing agent, an agent that interferes with a cell cycle checkpoint, a biphosphonate, or any combination thereof. A method of treating cancer comprising:
(A) administering to a patient suffering from cancer a therapeutically effective amount of at least one histone deacetylase inhibitor or a pharmaceutically acceptable derivative thereof;
(B) administering at least one other anti-cancer treatment when the expression level of the predetermined biomarker is within a predetermined range;
Including methods.   The cancer is breast cancer, colon cancer, colorectal cancer, non-small cell lung cancer, small cell lung cancer, liver cancer, ovarian cancer, prostate cancer, cervical cancer, bladder cancer, gastric cancer, gastrointestinal stromal tumor, pancreatic cancer, embryo Cellular tumor, mast cell tumor, neuroblastoma, mastocytosis, testicular cancer, glioblastoma, astrocytoma, lymphoma, melanoma, myeloma, acute myeloid leukemia (AML), acute lymphocytic leukemia ( ALL), myelodysplastic syndrome and chronic myeloid leukemia. Said at least one histone deacetylase inhibitor is of formula (I):
(Where
R ¹ is hydrogen or alkyl;
X is —O—, —NR ² —, or —S (O) _n, where n is 0-2 and R ² is hydrogen or alkyl;
Y is alkylene optionally substituted with cycloalkyl, optionally substituted phenyl, alkylthio, alkylsulfinyl, alkylsulfonyl, optionally substituted phenylalkylthio, optionally substituted phenylalkylsulfonyl, hydroxy, or optionally Substituted phenoxy,
Ar ¹ is phenylene or heteroarylene, wherein said Ar ¹ is optionally substituted with one or two groups independently selected from alkyl, halo, hydroxy, alkoxy, haloalkoxy or haloalkyl And
R ³ is hydrogen, alkyl, hydroxyalkyl, or optionally substituted phenyl;
Ar ² is aryl, aralkyl, aralkenyl, heteroaryl, heteroaralkyl, heteroaralkenyl, cycloalkyl, cycloalkylalkyl, heterocycloalkyl, or heterocycloalkylalkyl. )
The method according to claim 12, which has the following structure and is a single stereoisomer, a single geometric isomer or a mixture thereof, or a pharmaceutically acceptable salt thereof.   The method of claim 12, wherein the predetermined biomarker is RAD51.   21. The method of claim 20, wherein the predetermined biomarker is RAD51 lesion disruption.   16. The predetermined range of biomarker expression levels is less than 70% compared to the biomarker expression level prior to the administration of the at least one histone deacetylase inhibitor. Method.   The group wherein the at least one other anticancer treatment comprises radiation therapy, surgery, gene therapy, siRNA or RNAi therapy, administration of a therapeutically effective amount of at least one anticancer agent, or any combination thereof The method according to claim 12, selected from: A method of treating a disease, disorder or condition associated with a deficiency in non-homologous end joining of DNA comprising:
a) preventing the interaction of BRCA1 and RAD51 in a patient suffering from a disease, disorder or condition associated with a defect in non-homologous end joining of DNA, inhibiting the activity of at least one therapeutically effective amount of BRCA1; Or administering an agent that prevents the construction of a functional repair complex for homologous recombination involving BRCA1;
b) administering to said patient a treatment capable of damaging cellular DNA;
Including methods. A method of using a histone deacetylase inhibitor comprising:
(A) administering to the subject a therapeutically effective amount of at least one histone deacetylase inhibitor or a pharmaceutically acceptable derivative thereof;
(B) monitoring a change in the expression level of a predetermined biomarker in at least one cell of the subject;
(C) administering at least one other therapeutic measure when the expression level of the biomarker is within a predetermined range;
Including methods. A method of treating a disease, disorder or condition in which RAD51 is overexpressed, comprising:
(A) In patients with diseases, disorders or conditions that overexpress RAD51, inhibit the activity of at least one therapeutically effective amount of RAD51, prevent the formation of RAD51 foci, or homologous recombination of DNA Administering an agent that prevents the construction of a functional repair complex for
(B) administering to the patient a treatment capable of damaging cellular DNA;
Including methods. (A) a first agent that inhibits the activity of at least one therapeutically effective amount of RAD51, prevents the formation of RAD51 foci, or prevents the construction of a functional repair complex for homologous recombination of DNA. A first coating for one release;
(B) a second coating for a second release of at least one other therapeutic agent;
A pharmaceutical composition comprising   23. A pharmaceutical composition according to claim 22, wherein the agent that inhibits the activity of RAD51 is at least one histone deacetylase inhibitor, or a pharmaceutically acceptable derivative thereof. Said at least one histone deacetylase inhibitor is of formula (I):
(Where
R ¹ is hydrogen or alkyl;
X is —O—, —NR ² — or —S (O) _n, where n is 0-2 and R ² is hydrogen or alkyl;
Y is alkylene optionally substituted with cycloalkyl, optionally substituted phenyl, alkylthio, alkylsulfinyl, alkylsulfonyl, optionally substituted phenylalkylthio, optionally substituted phenylalkylsulfonyl, hydroxy, or optionally Substituted phenoxy,
Ar ¹ is phenylene or heteroarylene, wherein said Ar ¹ is optionally substituted with one or two groups independently selected from alkyl, halo, hydroxy, alkoxy, haloalkoxy or haloalkyl ,
R ³ is hydrogen, alkyl, hydroxyalkyl, or optionally substituted phenyl;
Ar ² is aryl, aralkyl, aralkenyl, heteroaryl, heteroaralkyl, heteroaralkenyl, cycloalkyl, cycloalkylalkyl, heterocycloalkyl, or heterocycloalkylalkyl. )
24. The pharmaceutical composition according to claim 23, which has the following structure and is a single stereoisomer, a single geometric isomer, or a mixture thereof, or a pharmaceutically acceptable salt thereof. A method of selecting a cancer treatment for a patient in need of cancer treatment, comprising:
a) determining the expression level of RAD51 mRNA, or RAD51 protein level in at least one cell from the patient;
b) When the expression level of RAD51 mRNA or the level of RAD51 protein in a biological sample exceeds the predetermined expression level of RAD51 mRNA or the level of RAD51, at least one histone deacetylase inhibitor is effective for treatment. To suggest and
Including methods.